prepare_Rd: spi.Rd:117-119: Dropping empty section \note
prepare_Rd: spi.Rd:123-125: Dropping empty section \seealso
Rd file 'spi.Rd':
  \examples lines wider than 100 characters:
     spi(7,"spi.txt",1963,2010,"Standardized Precipitation Index - Rio Grande do Norte State",1,"years","months")

These lines will be truncated in the PDF manual.
Running examples in ‘splitstackshape-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cSplit_f
> ### Title: Split Concatenated Cells in a data.frame or a data.table
> ### Aliases: cSplit_f
> 
> ### ** Examples
> 
> 
> ## Sample data. Change `n` to larger values to test on larger data
> set.seed(1)
> n <- 10
> mydf <- data.frame(id = sequence(n))
> mydf <- within(mydf, {
+   v3 <- do.call(paste, c(data.frame(matrix(sample(
+   letters, n*4, TRUE), ncol = 4)), sep = "_"))
+   v2 <- do.call(paste, c(data.frame(matrix(sample(
+   LETTERS, n*3, TRUE), ncol = 3)), sep = "."))
+   v1 <- do.call(paste, c(data.frame(matrix(sample(
+   10, n*2, TRUE), ncol = 2)), sep = "-"))
+ })
> mydf
   id   v1    v2      v3
1   1  4-5 V.M.X g_f_y_m
2   2  9-8 Q.W.H j_e_f_p
3   3  4-4 U.L.L o_r_q_m
4   4  4-4 O.G.I x_j_d_e
5   5  5-8 N.B.Q f_u_g_v
6   6  9-3 U.C.G x_m_k_r
7   7  9-8 A.I.M y_s_a_u
8   8  4-2 M.N.T r_z_j_c
9   9  8-3 T.R.C q_j_w_s
10 10 10-2 S.K.W b_u_i_k
> 
> cSplit_f(mydf, splitCols = c("v1", "v2", "v3"), sep = c("-", ".", "_"))
Error in fread(x, sep[i], header = FALSE) : 
  You can provide 'input=' or 'file=', not both.
Calls: cSplit_f -> fread
Execution halted
File ‘splus2R/libs/splus2R.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  all.equal.list all.equal.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
R2.global: no visible global function definition for ‘var’
calculer.var.exp: no visible global function definition for ‘var’
creer.noeud: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘var’
ponderer.classe: no visible global function definition for ‘cov’
spodt: no visible global function definition for ‘model.frame’
spodt.tree: no visible global function definition for ‘plot.new’
spodt.tree: no visible global function definition for ‘par’
spodt.tree: no visible global function definition for ‘plot.window’
spodt.tree: no visible global function definition for ‘text’
spodt.tree: no visible global function definition for ‘segments’
test.spodt: no visible global function definition for ‘model.frame’
test.spodt: no visible global function definition for ‘hist’
test.spodt: no visible global function definition for ‘abline’
tracer.noeud: no visible global function definition for ‘text’
tracer.noeud: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline cov hist model.frame par plot.new plot.window segments text
  var
Consider adding
  importFrom("graphics", "abline", "hist", "par", "plot.new",
             "plot.window", "segments", "text")
  importFrom("stats", "cov", "model.frame", "var")
to your NAMESPACE file.
File ‘SPODT/libs/SPODT.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Ell.Theta: no visible global function definition for ‘ell.theta’
confid.int.theta: no visible global function definition for ‘qchisq’
confid.int.theta : sim.c: no visible global function definition for
  ‘runif’
confid.int.theta: no visible global function definition for ‘quantile’
dd.est: no visible global function definition for ‘ecdf’
ks.sporm : Simul: no visible global function definition for ‘runif’
ks.stat: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘ecdf’
plotor: no visible global function definition for ‘plot’
test.theta: no visible global function definition for ‘ecdf’
test.theta : sim: no visible global function definition for ‘runif’
Undefined global functions or variables:
  ecdf ell.theta plot qchisq quantile runif
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "ecdf", "qchisq", "quantile", "runif")
to your NAMESPACE file.
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
fetch_NBAPlayerStatistics: no visible global function definition for
  ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  coef.Lifedata.MLE coef.deglmx.MLE logLik.Lifedata.MLE plot.MICsplines
  print.Lifedata.MLE print.deglmx print.summary.Lifedata.MLE sqrt.mat
  summary.Lifedata.MLE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'SlrArd.Rd':
  \usage lines wider than 90 characters:
     SlrArd(T, X, bias = TRUE, method = c("VB", "VBMacKay", "PX-VB"), control = list(), check.lb=TRUE, a0 = 0, b0 = 0, mu0 = 0, xi0 = 1)

These lines will be truncated in the PDF manual.
plot.SPRT: no visible global function definition for ‘par’
plot.SPRT: no visible global function definition for ‘plot’
plot.SPRT: no visible global function definition for ‘abline’
print.SPRT: no visible global function definition for ‘head’
Undefined global functions or variables:
  abline head par plot
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("utils", "head")
to your NAMESPACE file.
fssa20: no visible global function definition for ‘runif’
fssa2d: no visible global function definition for ‘runif’
fssa30: no visible global function definition for ‘runif’
fssa3d: no visible global function definition for ‘runif’
ssa20: no visible global function definition for ‘runif’
ssa2d: no visible global function definition for ‘runif’
ssa30: no visible global function definition for ‘runif’
ssa3d: no visible global function definition for ‘runif’
ssi20: no visible global function definition for ‘runif’
ssi2d: no visible global function definition for ‘runif’
ssi30: no visible global function definition for ‘runif’
ssi3d: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Rd file 'fssa30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssa3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of anisotropic 3D clusters with (1,1)-neighborhood")

Rd file 'fssi30.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,0)-neighborhood")

Rd file 'fssi3d.Rd':
  \examples lines wider than 100 characters:
     main="Relative frequency distribution in the z=17 slice\n of isotropic 3D clusters with (1,1)-neighborhood")

These lines will be truncated in the PDF manual.
File ‘SPSL/libs/SPSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
plotThin: no visible global function definition for ‘par’
plotThin: no visible global function definition for ‘dev.interactive’
plotThin: no visible global function definition for ‘plot’
plotThin: no visible global function definition for ‘hist’
thin: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  dev.interactive hist par plot write.csv
Consider adding
  importFrom("grDevices", "dev.interactive")
  importFrom("graphics", "hist", "par", "plot")
  importFrom("utils", "write.csv")
to your NAMESPACE file.
sGda : <anonymous>: no visible global function definition for ‘cov’
sortgene: no visible global function definition for ‘model.matrix’
Undefined global functions or variables:
  cov model.matrix
Consider adding
  importFrom("stats", "cov", "model.matrix")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RJDBC’ ‘RMySQL’ ‘RODBC’ ‘RPostgreSQL’ ‘RSQLite’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
cacheQuery: no visible global function definition for ‘read.csv’
cacheQuery: no visible global function definition for ‘write.csv’
Undefined global functions or variables:
  read.csv write.csv
Consider adding
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
SQN: no visible binding for global variable ‘median’
SQN: no visible global function definition for ‘quantile’
SQN.demo.data: no visible global function definition for ‘rnorm’
mix.qn: no visible global function definition for ‘ecdf’
mix.qn: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  ecdf median quantile rnorm
Consider adding
  importFrom("stats", "ecdf", "median", "quantile", "rnorm")
to your NAMESPACE file.
plot.srafit: no visible global function definition for ‘layout’
plot.srafit: no visible global function definition for ‘par’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘dnorm’
sraData : vartruncGauss : ff: no visible global function definition for
  ‘pnorm’
sraData : vartruncGauss: no visible global function definition for
  ‘uniroot’
sraPlotMean: no visible global function definition for ‘axis’
sraPlotMean: no visible global function definition for ‘points’
sraPlotMean: no visible global function definition for ‘lines’
sraPlotMeanResid: no visible global function definition for ‘axis’
sraPlotMeanResid: no visible global function definition for ‘abline’
sraPlotMeanResid: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘axis’
sraPlotVar: no visible global function definition for ‘points’
sraPlotVar: no visible global function definition for ‘lines’
sraPlotVarResid: no visible global function definition for ‘axis’
sraPlotVarResid: no visible global function definition for ‘abline’
sraPlotVarResid: no visible global function definition for ‘points’
sraPlotlegend: no visible global function definition for ‘legend’
sraStartingvalues : sraStartingvalues.mu0: no visible global function
  definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarA0: no visible global
  function definition for ‘rnorm’
sraStartingvalues : sraStartingvalues.logvarE0: no visible global
  function definition for ‘rnorm’
sraStartingvalues: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis dnorm layout legend lines par pnorm points rnorm uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "layout", "legend", "lines",
             "par", "points")
  importFrom("stats", "dnorm", "pnorm", "rnorm", "uniroot")
to your NAMESPACE file.
Found the following hidden files and directories:
  .Rapp.history
  inst/script/.Rapp.history
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
File ‘sROC/R/onload.R’:
  .onLoad calls:
    packageStartupMessage("sROC 0.1-2 loaded")

See section ‘Good practice’ in '?.onAttach'.

AUC : TrapezInt: no visible global function definition for ‘approx’
AUC : SimpsonInt: no visible global function definition for ‘approx’
CI.CDF: no visible global function definition for ‘qnorm’
bw.CDF: no visible global function definition for ‘sd’
bw.CDF: no visible global function definition for ‘IQR’
bw.CDF.pi: no visible global function definition for ‘sd’
bw.CDF.pi: no visible global function definition for ‘bw.nrd0’
bw.CDF.pi: no visible global function definition for ‘bw.nrd’
bw.CDF.pi: no visible global function definition for ‘bw.ucv’
bw.CDF.pi: no visible global function definition for ‘bw.bcv’
bw.CDF.pi: no visible global function definition for ‘bw.SJ’
bw.CDF.pi: no visible global function definition for ‘IQR’
plot.CDF: no visible global function definition for ‘plot.default’
plot.CDF: no visible global function definition for ‘lines’
plot.CDF: no visible global function definition for ‘polygon’
plot.ROC: no visible global function definition for ‘plot.default’
plot.ROC: no visible global function definition for ‘abline’
Undefined global functions or variables:
  IQR abline approx bw.SJ bw.bcv bw.nrd bw.nrd0 bw.ucv lines
  plot.default polygon qnorm sd
Consider adding
  importFrom("graphics", "abline", "lines", "plot.default", "polygon")
  importFrom("stats", "IQR", "approx", "bw.SJ", "bw.bcv", "bw.nrd",
             "bw.nrd0", "bw.ucv", "qnorm", "sd")
to your NAMESPACE file.
Rd file 'CI.CDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kCDF.Rd':
  \examples lines wider than 100 characters:
     curve(pnorm(x, mean=-2, sd=1)/2 + pnorm(x, mean=3, sd=0.8)/2, from =-6, to=6, add=TRUE, lty=2, col="blue")

Rd file 'kROC.Rd':
  \usage lines wider than 90 characters:
     kROC(x, y, bw.x="pi_ucv", bw.y="pi_ucv", adjust=1, kernel=c("normal", "epanechnikov"), xgrid, 

These lines will be truncated in the PDF manual.
File ‘sROC/libs/sROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'::' or ':::' imports not declared from:
  ‘DBI’ ‘stringr’
File ‘ssa/libs/ssa.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
ssd : correction_method_D: no visible global function definition for
  ‘rnorm’
ssd : generate_bootstrap: no visible global function definition for
  ‘rmultinom’
ssd : bootstrap_method: no visible global function definition for
  ‘median’
ssd : bootstrap_method: no visible global function definition for
  ‘quantile’
ssd : unbalanced_generate_bootstrap: no visible global function
  definition for ‘rmultinom’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘median’
ssd : unbalanced_bootstrap_method: no visible global function
  definition for ‘quantile’
ssd: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  median qchisq quantile rmultinom rnorm
Consider adding
  importFrom("stats", "median", "qchisq", "quantile", "rmultinom",
             "rnorm")
to your NAMESPACE file.
L_hNV: no visible global function definition for ‘pnorm’
L_hNV_rho: no visible global function definition for ‘pnorm’
eff.ssfa: no visible global function definition for ‘pnorm’
plot_fitted: no visible global function definition for ‘lines’
plot_moran: no visible global function definition for ‘residuals’
print.summary.ssfa: no visible global function definition for
  ‘printCoefmat’
ssfa: no visible global function definition for ‘model.frame’
ssfa: no visible global function definition for ‘model.response’
ssfa.fit: no visible global function definition for ‘lm’
ssfa.fit: no visible global function definition for ‘var’
ssfa.fit: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pnorm’
summary.ssfa: no visible global function definition for ‘logLik’
summary.ssfa: no visible global function definition for ‘pchisq’
summary.ssfa: no visible binding for global variable ‘df’
u.ssfa: no visible global function definition for ‘dnorm’
u.ssfa: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  df dnorm lines lm logLik model.frame model.response pchisq pnorm
  printCoefmat residuals var
Consider adding
  importFrom("graphics", "lines")
  importFrom("stats", "df", "dnorm", "lm", "logLik", "model.frame",
             "model.response", "pchisq", "pnorm", "printCoefmat",
             "residuals", "var")
to your NAMESPACE file.
Package in Depends field not imported from: ‘survey’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fit.model: no visible global function definition for ‘hadamard’
Undefined global functions or variables:
  hadamard
mem.usage: no visible global function definition for ‘read.delim’
Undefined global functions or variables:
  read.delim
Consider adding
  importFrom("utils", "read.delim")
to your NAMESPACE file.
sslCoTrain: no visible global function definition for ‘predict’
sslSelfTrain: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘SSL/libs/SSL.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  coef.heckit5rob coef.heckitrob fitted.heckit5rob fitted.heckitrob
  print.heckit5rob print.heckitrob print.summary.heckit5rob
  print.summary.heckitrob residuals.heckit5rob residuals.heckitrob
  summary.heckit5rob summary.heckitrob vcov.heckit5rob vcov.heckitrob
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
map.world: no visible global function definition for ‘par’
map.world: no visible global function definition for ‘plot.new’
map.world: no visible global function definition for ‘plot.window’
map.world: no visible global function definition for ‘lines’
map.world: no visible global function definition for ‘title’
map.world: no visible global function definition for ‘axis’
map.world: no visible global function definition for ‘box’
plot.smooth.sspline: no visible global function definition for
  ‘predict’
plot.smooth.sspline: no visible global function definition for
  ‘filled.contour’
plot.smooth.sspline: no visible binding for global variable
  ‘terrain.colors’
plot.smooth.sspline: no visible global function definition for ‘title’
plot.smooth.sspline: no visible global function definition for ‘axis’
station: no visible binding for global variable ‘WTdiff’
station: no visible global function definition for ‘points’
Undefined global functions or variables:
  WTdiff axis box filled.contour lines par plot.new plot.window points
  predict terrain.colors title
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "axis", "box", "filled.contour", "lines", "par",
             "plot.new", "plot.window", "points", "title")
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘sspline/libs/sspline.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
SS.ID: no visible global function definition for ‘var’
SS.sim.chol: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm var
Consider adding
  importFrom("stats", "rnorm", "var")
to your NAMESPACE file.
error.est : <anonymous>: no visible global function definition for
  ‘median’
holm.robust: no visible global function definition for ‘pnorm’
holm.robust: no visible global function definition for ‘median’
holm.robust: no visible global function definition for ‘mad’
huberize: no visible global function definition for ‘quantile’
ssvd.initial: no visible global function definition for ‘mad’
ssvd.iter.thresh: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad median pnorm quantile
Consider adding
  importFrom("stats", "mad", "median", "pnorm", "quantile")
to your NAMESPACE file.
File ‘stable/libs/stable.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.ls.objects: no visible binding for global variable ‘object.size’
Undefined global functions or variables:
  object.size
Consider adding
  importFrom("utils", "object.size")
to your NAMESPACE file.
.expandLevels: no visible global function definition for ‘na.omit’
.ffStack: no visible global function definition for ‘na.omit’
.ffffStack: no visible global function definition for ‘na.omit’
Stack : <anonymous>: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-data.frame: no visible global function definition for
  ‘na.omit’
ffStack,ffdf-ffdf: no visible global function definition for ‘na.omit’
ffStack,ffdf-list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
genericPlot: no visible global function definition for ‘dev.new’
genericPlot: no visible global function definition for ‘par’
genericPlot: no visible global function definition for ‘rainbow’
genericPlot: no visible global function definition for ‘plot’
genericPlot: no visible global function definition for ‘lines’
genericPlot: no visible global function definition for ‘legend’
genericPlot: no visible global function definition for ‘dev.copy2pdf’
genericPlot: no visible global function definition for ‘dev.copy2eps’
genericPlot: no visible global function definition for ‘dev.print’
genericPlot: no visible binding for global variable ‘png’
genericPlot: no visible binding for global variable ‘tiff’
plotStrains: no visible global function definition for ‘rainbow’
plotStrains: no visible global function definition for ‘dev.new’
plotStrains: no visible global function definition for ‘par’
plotStrains: no visible global function definition for ‘plot’
plotStrains: no visible global function definition for ‘lines’
plotStrains: no visible global function definition for ‘legend’
plotStrains: no visible global function definition for ‘dev.copy2pdf’
plotStrains: no visible global function definition for ‘dev.copy2eps’
plotStrains: no visible global function definition for ‘dev.print’
plotStrains: no visible binding for global variable ‘png’
plotStrains: no visible binding for global variable ‘tiff’
Undefined global functions or variables:
  dev.copy2eps dev.copy2pdf dev.new dev.print legend lines par plot png
  rainbow tiff
Consider adding
  importFrom("grDevices", "dev.copy2eps", "dev.copy2pdf", "dev.new",
             "dev.print", "png", "rainbow", "tiff")
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Licence’
'library' or 'require' calls to packages already attached by Depends:
  ‘np’ ‘sp’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘np’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.

Found the following calls to attach():
File ‘stam/R/stkde.sig.r’:
  attach(samdata)
See section ‘Good practice’ in ‘?attach’.
Rd file 'stkde.sig.rd':
  \examples lines wider than 100 characters:
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=1))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken
     system.time(stkde.sig(d[,1],d[,2],d[,3],xgrids=20,ygrids=20,breaks=0.05,sim=3,alpha=0.05,nrowspar=2))
     #determines how much real and CPU time (in seconds) the currently running R process has already taken

These lines will be truncated in the PDF manual.
find.names: no visible global function definition for ‘na.omit’
generate.names: no visible global function definition for ‘na.omit’
standardize.countrynames: no visible global function definition for
  ‘data’
standardize.names: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.
Rd file 'standardize.countrynames.Rd':
  \usage lines wider than 90 characters:
     standardize.countrynames(input, input.column = NULL, standard = "default", standard.column = NULL, only.names = FALSE, na.rm = FALSE, s ... [TRUNCATED]

Rd file 'standardize.text.Rd':
  \usage lines wider than 90 characters:
     standardize.text(input, input.column = NULL, standard, standard.column = NULL, regex = NULL, codes = NULL, match = FALSE, only.names =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘starma/libs/starma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘codetools’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘codetools’ ‘gss’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘STAR/libs/STAR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following hidden files and directories:
  inst/.Renviron.d
  inst/.Rprofile.d
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘StatCharrms.tex’ failed.
LaTeX errors:
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘statcomp/libs/statcomp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘statcomp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: global_complexity
> ### Title: A function to compute global information and complexity measures
> ###   for time series
> ### Aliases: global_complexity
> 
> ### ** Examples
> 
> x = arima.sim(model=list(ar = 0.3), n = 10^4)
> global_complexity(x = x, ndemb = 6)
        PE    MPR_Cjs  nforbiden 
0.98413890 0.03714999 0.00000000 
> # or:
> opd = ordinal_pattern_distribution(x = x, ndemb = 6)
> global_complexity(opd = opd, ndemb = 6)
Error in if (is.na(opd)) opd = ordinal_pattern_distribution(x = x, ndemb = ndemb) : 
  the condition has length > 1
Calls: global_complexity
Execution halted
Found the following apparent S3 methods exported but not registered:
  print.corsign
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
actvspred: no visible global function definition for ‘quantile’
actvspred: no visible global function definition for ‘aggregate’
actvspred: no visible global function definition for ‘par’
actvspred: no visible global function definition for ‘plot’
actvspred: no visible global function definition for ‘lines’
auc: no visible global function definition for ‘par’
auc: no visible global function definition for ‘plot’
decile: no visible global function definition for ‘quantile’
dqcontinuous : numoutliers: no visible global function definition for
  ‘quantile’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘sd’
dqcontinuous : <anonymous>: no visible global function definition for
  ‘quantile’
gini: no visible global function definition for ‘par’
gini: no visible global function definition for ‘plot’
gini: no visible global function definition for ‘abline’
iv: no visible global function definition for ‘quantile’
iv: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘aggregate’
ks: no visible global function definition for ‘par’
ks: no visible global function definition for ‘plot’
ks: no visible global function definition for ‘lines’
outliers: no visible global function definition for ‘quantile’
outliers: no visible global function definition for ‘na.omit’
pentile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline aggregate lines na.omit par plot quantile sd
Consider adding
  importFrom("graphics", "abline", "lines", "par", "plot")
  importFrom("stats", "aggregate", "na.omit", "quantile", "sd")
to your NAMESPACE file.
inspect: no visible global function definition for ‘par’
inspect: no visible global function definition for ‘abline’
inspect: no visible global function definition for ‘lines’
inspect: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘dev.off’
plotfit: no visible global function definition for ‘par’
plotfit: no visible global function definition for ‘lines’
plotfit: no visible global function definition for ‘points’
plotfit: no visible global function definition for ‘legend’
plothill: no visible global function definition for ‘par’
plothill: no visible global function definition for ‘abline’
plothill: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘par’
plotmultifit: no visible global function definition for ‘lines’
plotmultifit: no visible global function definition for ‘points’
plotmultifit: no visible global function definition for ‘pexp’
plotmultifit: no visible global function definition for ‘plnorm’
plotmultifit: no visible global function definition for ‘ppois’
plotmultifit: no visible global function definition for ‘legend’
plotols: no visible global function definition for ‘dev.off’
plotols: no visible global function definition for ‘lm’
plotols: no visible global function definition for ‘par’
plotols: no visible global function definition for ‘abline’
plotols: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline dev.off legend lines lm par pexp plnorm points ppois
Consider adding
  importFrom("grDevices", "dev.off")
  importFrom("graphics", "abline", "legend", "lines", "par", "points")
  importFrom("stats", "lm", "pexp", "plnorm", "ppois")
to your NAMESPACE file.
File ‘staTools/libs/staTools.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘STB/libs/STB.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘steadyICA/libs/steadyICA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
getStp: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘plot’
plot.steeptest: no visible global function definition for ‘axis’
plot.steeptest: no visible global function definition for ‘box’
plot.steeptest: no visible global function definition for ‘lm’
plot.steeptest: no visible global function definition for ‘abline’
plot.steeptest: no visible global function definition for ‘legend’
plot.steeptest: no visible global function definition for
  ‘as.graphicsAnnot’
steeptest: no visible global function definition for ‘lm’
summary.steeptest: no visible global function definition for ‘var’
summary.steeptest: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline as.graphicsAnnot axis box legend lm plot quantile var
Consider adding
  importFrom("grDevices", "as.graphicsAnnot")
  importFrom("graphics", "abline", "axis", "box", "legend", "plot")
  importFrom("stats", "lm", "quantile", "var")
to your NAMESPACE file.
File ‘steepness/libs/steepness.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Stem.Bootstrap: no visible global function definition for ‘runif’
filtering: no visible global function definition for ‘is.ts’
filtering: no visible global function definition for ‘ts’
filtering: no visible global function definition for ‘start’
filtering: no visible global function definition for ‘end’
filtering: no visible global function definition for ‘frequency’
kalman: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘is.ts’
smoothing: no visible global function definition for ‘ts’
smoothing: no visible global function definition for ‘start’
smoothing: no visible global function definition for ‘end’
smoothing: no visible global function definition for ‘frequency’
Undefined global functions or variables:
  end frequency is.ts runif start ts
Consider adding
  importFrom("stats", "end", "frequency", "is.ts", "runif", "start",
             "ts")
to your NAMESPACE file.
Running examples in ‘stepPenal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: StepPenal
> ### Title: Stepwise forward variable selection using penalized regression.
> ### Aliases: StepPenal
> 
> ### ** Examples
> 
> # use the StepPenal function on a simulated dataset, with given lamda and w.
> 
> set.seed(14)
> beta    <- c(3, 2, -1.6, -4)
> noise   <- 5
> simData <- SimData(N=100, beta=beta, noise=noise, corr=FALSE)
> 
> before <- Sys.time()
> stepPenal<- StepPenal(Data=simData, lamda=1.5, w=0.1)
Error in if (!is.na(useoptim)) { : the condition has length > 1
Calls: StepPenal
Execution halted
File ‘stepp/libs/stepp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘stepwise/libs/stepwise.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘StepwiseTest/libs/StepwiseTest.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
d1spectrum: no visible global function definition for ‘fft’
d2spectrum: no visible global function definition for ‘fft’
plot.d1nat: no visible global function definition for ‘plot’
plot.d1nat: no visible global function definition for ‘lines’
plot.d1nat: no visible global function definition for ‘legend’
plot.d1nat: no visible global function definition for ‘title’
plot.d1spec: no visible global function definition for ‘plot’
plot.d1spec: no visible global function definition for ‘lines’
plot.d1spec: no visible global function definition for ‘legend’
plot.d1spec: no visible global function definition for ‘title’
plot.d2spec: no visible global function definition for ‘plot’
plot.d2spec: no visible global function definition for ‘lines’
plot.d2spec: no visible global function definition for ‘legend’
plot.d2spec: no visible global function definition for ‘title’
plot.pvalign: no visible global function definition for ‘plot’
plot.pvalign: no visible global function definition for ‘lines’
plot.pvalign: no visible global function definition for ‘legend’
plot.pvalign: no visible global function definition for ‘title’
print.d1nat: no visible global function definition for ‘plot’
print.d1spec: no visible global function definition for ‘plot’
print.d2spec: no visible global function definition for ‘plot’
print.pvalign: no visible global function definition for ‘plot’
utild1bin: no visible global function definition for ‘median’
utild1bin: no visible global function definition for ‘sd’
utild1clean: no visible global function definition for ‘sd’
utild1filt: no visible global function definition for ‘convolve’
Undefined global functions or variables:
  convolve fft legend lines median plot sd title
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "title")
  importFrom("stats", "convolve", "fft", "median", "sd")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  na.stinterp.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
na.stinterp.default: no visible global function definition for ‘time’
na.stinterp.default: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit time
Consider adding
  importFrom("stats", "na.omit", "time")
to your NAMESPACE file.
Running examples in ‘stinepack-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: na.stinterp
> ### Title: Replace NAs by Stineman interpolation
> ### Aliases: na.stinterp na.stinterp.default
> ### Keywords: ts
> 
> ### ** Examples
> 
> na.stinterp(c(2,NA,1,4,5,2))
Error in UseMethod("na.stinterp") : 
  no applicable method for 'na.stinterp' applied to an object of class "c('double', 'numeric')"
Calls: na.stinterp
Execution halted
File ‘stlplus/libs/stlplus.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
myQQNorm: no visible global function definition for ‘mad’
myQQNorm: no visible global function definition for ‘qnorm’
myQQNorm: no visible global function definition for ‘plot’
myQQNorm: no visible global function definition for ‘matlines’
myQQNorm: no visible global function definition for ‘points’
myQQNorm: no visible global function definition for ‘qqline’
myQQNorm: no visible global function definition for ‘box’
qqnormSim,lm: no visible global function definition for ‘resid’
Undefined global functions or variables:
  box mad matlines plot points qnorm qqline resid
Consider adding
  importFrom("graphics", "box", "matlines", "plot", "points")
  importFrom("stats", "mad", "qnorm", "qqline", "resid")
to your NAMESPACE file.
File ‘StMoSim/libs/StMoSim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'calc.stoich.coef.Rd':
  \usage lines wider than 90 characters:
     calc.stoich.coef(alpha, name, subst, subst.norm, nu.norm = 1, constraints = list(), eps = 1e-5, verbose = TRUE)

These lines will be truncated in the PDF manual.
'::' or ':::' imports not declared from:
  ‘RPostgreSQL’ ‘RPostgres’ ‘base64enc’
'library' or 'require' calls not declared from:
  ‘RPostgreSQL’ ‘RPostgres’
Packages in Depends field not imported from:
  ‘cubature’ ‘deldir’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.devresid plot.gridresid plot.stpp plot.superthin plot.supresid
  plot.tessdev plot.tessresid plot.thinresid print.devresid
  print.gridresid print.stgrid print.stpp print.stwin print.superthin
  print.supresid print.tessdev print.tessresid print.thinresid
  summary.superthin summary.supresid summary.thinresid
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'gridresid.Rd':
  \usage lines wider than 90 characters:
     gridresid(X, cifunction, theta = NULL, lambda = NULL, grid = c(10, 10), gf = NULL, resid = c("raw", "pearson", "inverse"), algthm = c(" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running examples in ‘stppResid-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gridresid
> ### Title: Calculate grid-based residuals
> ### Aliases: gridresid
> 
> ### ** Examples
> 
> #===> load simulated data <===#
> data(simdata)
> X <- stpp(simdata$x, simdata$y, simdata$t)
stw missing - using default space-time window [0, 1]x[0, 1]
> 
> #===> define two conditional intensity functions <===#
> ci1 <- function(X, theta){theta*exp(-2*X$x - 2*X$y - 2*X$t)} #correct model
> 
> ci2 <- function(X, theta = NULL){rep(250, length(X$x))} #homogeneous Poisson model
> 
> ## Not run: 
> ##D gresiduals <- gridresid(X, ci1, theta = 3000)
> ##D plot(gresiduals)
> ## End(Not run)
> gresiduals2 <- gridresid(X, ci2)
> plot(gresiduals2)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot -> plot.default -> xy.coords
Execution halted
StratPhyloCongruence: no visible global function definition for ‘runif’
StratPhyloCongruence: no visible global function definition for
  ‘txtProgressBar’
StratPhyloCongruence: no visible global function definition for
  ‘setTxtProgressBar’
StratPhyloCongruence: no visible global function definition for ‘pnorm’
StratPhyloCongruence: no visible global function definition for ‘sd’
geoscalePhylo: no visible global function definition for ‘data’
geoscalePhylo: no visible global function definition for ‘par’
geoscalePhylo: no visible global function definition for ‘text’
geoscalePhylo: no visible global function definition for ‘segments’
geoscalePhylo: no visible global function definition for ‘rect’
geoscalePhylo: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  data par pnorm rect rgb runif sd segments setTxtProgressBar text
  txtProgressBar
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "rect", "segments", "text")
  importFrom("stats", "pnorm", "runif", "sd")
  importFrom("utils", "data", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
File ‘strat/libs/strat.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.icweib print.icweib
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
HRatio: no visible global function definition for ‘qnorm’
icweib: no visible global function definition for ‘model.frame’
icweib: no visible binding for global variable ‘na.pass’
icweib: no visible global function definition for ‘complete.cases’
icweib: no visible global function definition for ‘model.matrix’
icweib: no visible global function definition for ‘optim’
icweib: no visible global function definition for ‘pchisq’
icweib: no visible global function definition for ‘pnorm’
plot.icweib : getstat: no visible global function definition for
  ‘qnorm’
plot.icweib: no visible global function definition for ‘plot’
plot.icweib: no visible global function definition for ‘lines’
plot.icweib: no visible global function definition for ‘legend’
print.icweib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
Running examples in ‘straweib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.icweib
> ### Title: Plot estimated survival function
> ### Aliases: plot.icweib
> 
> ### ** Examples
> 
> data(tooth24)
> fit <- icweib(L = left, R = right, data = tooth24, strata = dmf, covariates = ~sex)
> surv <- plot(fit, Z = 1, tRange = c(1, 7), tEst=1:7, xlab = "Time", ylab = "Survival Function", 
+      main = "Estimated survival function for sex = 1 (girls)")
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
breakpoints.formula: no visible global function definition for
  ‘%dopar%’
breakpoints.formula: no visible binding for global variable ‘i’
efpFunctional: multiple local function definitions for ‘plotProcess’
  with different formal arguments
mefp.efp: multiple local function definitions for ‘computeEmpProc’ with
  different formal arguments
sctest.default: no visible global function definition for ‘tail’
Undefined global functions or variables:
  %dopar% i tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Running examples in ‘StructFDR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: StructFDR
> ### Title: False Discovery Rate (FDR) Control Integrating a General Prior
> ###   Structure
> ### Aliases: StructFDR
> ### Keywords: Multiple testing False discovery rate Genetics Metagenomics
> ###   Genomics
> 
> ### ** Examples
> 
> require(ape) 
> require(nlme)
> require(cluster)
> require(StructFDR)
> 
> # Generate a caelescence tree and partition into 10 clusters
> set.seed(1234)
> n <- 20
> p <- 200
> tree <- rcoal(p)
> # Pairwise distance matrix. 
> D <- cophenetic(tree)
> clustering <- pam(D, k=10)$clustering
> 
> # Simulate case-control data, assuming cluster 2 is differential  
> X.control <- matrix(rnorm(n*p), p, n)
> X.case <- matrix(rnorm(n*p), p, n)
> eff.size <- rnorm(sum(clustering == 2), 0.5, 0.2)     
> X.case[clustering == 2, ] <- X.case[clustering == 2, ] + eff.size
> X <- cbind(X.control, X.case)
> Y <- gl(2, n) 
> 
> # Define testing and permutation function
> test.func <- function (X, Y) {
+ 	obj <- apply(X, 1, function(x) {
+ 				ttest.obj <- t.test(x ~ Y)
+ 				c(ttest.obj$p.value, sign(ttest.obj$statistic))
+ 			})
+     return(list(p.value=obj[1, ], e.sign=obj[2, ]))
+ }
> 
> perm.func <- function (X, Y) {
+ 	return(list(X=X, Y=sample(Y)))
+ }
> 
> # Call StructFDR
> tree.fdr.obj <- StructFDR(X, Y, D, test.func, perm.func)
Warning in StructFDR(X, Y, D, test.func, perm.func) :
  Both the data matrix and the distance matrix should have labels (rownames) to avoid potential errors!

Test on original data sets  ...
Test on permuted data sets  ...
Error in if (alt.FDR == "Permutation") { : the condition has length > 1
Calls: StructFDR
Execution halted
PlotHypTree: no visible global function definition for ‘browseURL’
treePValues: no visible global function definition for ‘lm’
treePValues: no visible global function definition for ‘pf’
plot,GBH-ANY: no visible binding for global variable ‘sorted.hyp’
plot,GBH-ANY: no visible binding for global variable ‘pval’
plot,GBH-ANY: no visible binding for global variable ‘group’
plot,GBH-ANY: no visible binding for global variable ‘type’
Undefined global functions or variables:
  browseURL group lm pf pval sorted.hyp type
Consider adding
  importFrom("stats", "lm", "pf")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
Running examples in ‘structSSI-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: EstimatedHFDRControl
> ### Title: Estimate FDR control variations for HFDR procedure
> ### Aliases: EstimatedHFDRControl
> ### Keywords: ~htest
> 
> ### ** Examples
> 
> library('igraph')

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> library('ape')

Attaching package: ‘ape’

The following objects are masked from ‘package:igraph’:

    edges, mst, ring

> 
> alternative.indices <- sample(1:49, 30)
> unadj.p.values <- vector("numeric", length = 49)
> unadj.p.values[alternative.indices] <- runif(30, 0, 0.01)
> unadj.p.values[-alternative.indices] <- runif(19, 0, 1)
> unadj.p.values[c(1:5)] <- runif(5, 0, 0.01)
> names(unadj.p.values) <- paste("Hyp ", c(1:49))
> 
> tree <- as.igraph(rtree(25))
Error in UseMethod("as.igraph") : 
  no applicable method for 'as.igraph' applied to an object of class "phylo"
Calls: as.igraph
Execution halted
Running ‘testGBHProcedures.R’ [4s/7s]
  Running ‘testHierarchicalMethods.R’ [4s/6s]
Running the tests in ‘tests/testHierarchicalMethods.R’ failed.
Complete output:
  > ## Test the hypothesesTree creation class.
  > 
  > set.seed(130229)
  > library('structSSI')
  > library('ape')
  > library('igraph')
  
  Attaching package: 'igraph'
  
  The following objects are masked from 'package:ape':
  
      edges, mst, ring
  
  The following objects are masked from 'package:stats':
  
      decompose, spectrum
  
  The following object is masked from 'package:base':
  
      union
  
  > tree.1 <- as.igraph(rtree(10))
  Error in UseMethod("as.igraph") : 
    no applicable method for 'as.igraph' applied to an object of class "phylo"
  Calls: as.igraph
  Execution halted
File ‘strum/libs/strum.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Warning: no function found corresponding to methods exports from ‘stsm.class’ for: ‘show’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
stsm.model: no visible global function definition for ‘is.ts’
stsm.model: no visible global function definition for ‘var’
stsm.model: no visible global function definition for ‘frequency’
stsm.model: no visible global function definition for ‘na.omit’
stsm.model: no visible global function definition for ‘fft’
stsm.model: no visible global function definition for ‘new’
stsm.sgf: no visible global function definition for ‘frequency’
char2numeric,stsm: no visible global function definition for
  ‘frequency’
set.cpar,stsm: no visible global function definition for ‘validObject’
set.nopars,stsm: no visible global function definition for
  ‘validObject’
set.pars,stsm: no visible global function definition for ‘validObject’
transPars,stsm: no visible global function definition for ‘var’
Undefined global functions or variables:
  fft frequency is.ts na.omit new validObject var
Consider adding
  importFrom("methods", "new", "validObject")
  importFrom("stats", "fft", "frequency", "is.ts", "na.omit", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
File ‘stsm/libs/stsm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call not declared from: ‘DiagrammeR’
Found the following apparent S3 methods exported but not registered:
  predict.sublasso
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
SubLasso: no visible global function definition for ‘predict’
SubLasso: no visible global function definition for ‘coef’
SubLasso: no visible global function definition for ‘dev.new’
SubLasso: no visible global function definition for ‘cor’
SubLasso: no visible global function definition for ‘boxplot’
predict.sublasso: no visible global function definition for ‘predict’
Undefined global functions or variables:
  boxplot coef cor dev.new predict
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "boxplot")
  importFrom("stats", "coef", "cor", "predict")
to your NAMESPACE file.
identifyGraph: no visible global function definition for ‘phyper’
mytriangle: no visible global function definition for ‘symbols’
plotGraph: no visible global function definition for ‘par’
plotGraph: no visible global function definition for ‘plot’
updateOrgEnvir: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  par phyper plot read.table symbols
Consider adding
  importFrom("graphics", "par", "plot", "symbols")
  importFrom("stats", "phyper")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.subsemble
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
predict.subsemble: no visible global function definition for ‘predict’
predict.subsemble: no visible binding for global variable ‘family’
subsemble: no visible global function definition for ‘gaussian’
subsemble: no visible global function definition for ‘detectCores’
subsemble : .make_Z_l: no visible global function definition for
  ‘parSapply’
subsemble : .make_Z_l: no visible global function definition for
  ‘makeCluster’
subsemble : .make_Z_l: no visible global function definition for
  ‘stopCluster’
subsemble: no visible global function definition for ‘parSapply’
subsemble: no visible global function definition for ‘makeCluster’
subsemble: no visible global function definition for ‘stopCluster’
subsemble: no visible global function definition for ‘predict’
Undefined global functions or variables:
  detectCores family gaussian makeCluster parSapply predict stopCluster
Consider adding
  importFrom("stats", "family", "gaussian", "predict")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘ROCR’ ‘penalized’
  Please remove these calls from your code.
ELF: no visible global function definition for ‘pt’
ELF: no visible global function definition for ‘qnorm’
ELF: no visible global function definition for ‘lm’
ELF: no visible global function definition for ‘lowess’
ELF: no visible global function definition for ‘dnorm’
ELF: no visible global function definition for ‘approx’
subtype: no visible global function definition for ‘runif’
subtype: no visible global function definition for ‘hclust’
subtype: no visible global function definition for ‘dist’
subtype: no visible global function definition for ‘cutree’
subtype: no visible global function definition for ‘pt’
subtype: no visible global function definition for ‘heatmap’
test_subtype_only: no visible global function definition for ‘pt’
test_subtype_only: no visible global function definition for ‘survdiff’
test_subtype_only: no visible global function definition for ‘survfit’
test_subtype_only: no visible global function definition for ‘title’
ufun: no visible global function definition for ‘dnorm’
ufun: no visible global function definition for ‘lowess’
Undefined global functions or variables:
  approx cutree dist dnorm hclust heatmap lm lowess pt qnorm runif
  survdiff survfit title
Consider adding
  importFrom("graphics", "title")
  importFrom("stats", "approx", "cutree", "dist", "dnorm", "hclust",
             "heatmap", "lm", "lowess", "pt", "qnorm", "runif")
to your NAMESPACE file.
Rd file 'subtype.Rd':
  \usage lines wider than 90 characters:
     subtype(GEset, outcomeLabels, treatment=NULL, Npermutes=10, Nchunks = 25, minClusterSizeB = 20, NclustersASet = 100, FDRpermutation = T ... [TRUNCATED]
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

Rd file 'summary.Rd':
  \examples lines wider than 100 characters:
     summary(A,f.out=0)  ### f.out can be used for filtering out uninteresting subtypes. e.g. if f.out=2, we ignore subtypes having N01_0<=2 ... [TRUNCATED]

These lines will be truncated in the PDF manual.
playSudoku : replot: no visible global function definition for ‘par’
playSudoku : replot: no visible global function definition for ‘plot’
playSudoku : replot: no visible global function definition for
  ‘segments’
playSudoku : replot: no visible global function definition for ‘text’
playSudoku: no visible global function definition for ‘tktoplevel’
playSudoku: no visible global function definition for ‘tkwm.title’
playSudoku: no visible global function definition for ‘tkrplot’
playSudoku: no visible global function definition for ‘tktext’
playSudoku: no visible global function definition for ‘tkscrollbar’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkyview’
playSudoku: no visible global function definition for ‘tkconfigure’
playSudoku : <anonymous>: no visible global function definition for
  ‘tkset’
playSudoku: no visible global function definition for ‘tkpack’
playSudoku: no visible global function definition for ‘tcl’
playSudoku: no visible global function definition for ‘tkcget’
playSudoku : showz: no visible global function definition for
  ‘tkrreplot’
playSudoku : type: no visible global function definition for ‘tkinsert’
playSudoku : type: no visible global function definition for ‘tksee’
playSudoku : kb: no visible global function definition for ‘tkdestroy’
playSudoku: no visible global function definition for
  ‘getGraphicsEvent’
playSudoku: no visible global function definition for ‘tkbind’
playSudoku: no visible global function definition for ‘tkwait.window’
Undefined global functions or variables:
  getGraphicsEvent par plot segments tcl text tkbind tkcget tkconfigure
  tkdestroy tkinsert tkpack tkrplot tkrreplot tkscrollbar tksee tkset
  tktext tktoplevel tkwait.window tkwm.title tkyview
Consider adding
  importFrom("grDevices", "getGraphicsEvent")
  importFrom("graphics", "par", "plot", "segments", "text")
to your NAMESPACE file.
SUE.fitted.values: no visible global function definition for
  ‘model.frame’
SUE.lm: no visible global function definition for ‘model.frame’
SUE.lm: no visible global function definition for ‘lm’
SUE.lm: no visible global function definition for ‘anova’
SUE.plot: no visible global function definition for ‘plot’
SUE.residuals: no visible global function definition for ‘model.frame’
parameters : para2: no visible global function definition for ‘uniroot’
parameters: no visible global function definition for ‘optimize’
parameters: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  anova lm model.frame optimize plot uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "anova", "lm", "model.frame", "optimize",
             "uniroot")
to your NAMESPACE file.
Rd file 'SUE.lm.Rd':
  \examples lines wider than 100 characters:
     ##We analysis the well known stackloss data by using ordinary linear method and the subsampling method. 
     ##proportion of outliers in the data. The subsample size is chosen to be the default size of ns = 11.
     plot(SUE.fitted.values(a2),SUE.residuals(a2),xlab="(b) fitted values",ylab="residuals",ylim=c(-12,12))
     plot(SUE.fitted.values(a3),SUE.residuals(a3),xlab="(c) fitted values",ylab="residuals",ylim=c(-12,12))

These lines will be truncated in the PDF manual.
MCMCCV: no visible global function definition for ‘rnorm’
MLCVGauss: no visible global function definition for ‘runif’
MLCVGauss: no visible global function definition for ‘optim’
SimSunderData: no visible global function definition for ‘runif’
SimSunderData: no visible global function definition for ‘dist’
SimSunderData: no visible global function definition for ‘rnorm’
SimSunderData: no visible global function definition for ‘qgamma’
SimSunderData: no visible global function definition for ‘pnorm’
SimSunderData: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  dist optim pnorm qgamma rmultinom rnorm runif
Consider adding
  importFrom("stats", "dist", "optim", "pnorm", "qgamma", "rmultinom",
             "rnorm", "runif")
to your NAMESPACE file.
File ‘Sunder/libs/Sunder.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
sunter: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
supcluster : itgamma: no visible global function definition for
  ‘rgamma’
supcluster : itgamma: no visible global function definition for
  ‘dgamma’
supcluster : itgamma: no visible global function definition for ‘runif’
supcluster : itbeta: no visible global function definition for ‘rnorm’
supcluster : itbeta: no visible global function definition for ‘runif’
supcluster : itj: no visible global function definition for ‘dmultinom’
supcluster: no visible global function definition for ‘kmeans’
tab1: no visible global function definition for ‘image’
tab1: no visible global function definition for ‘gray’
tab1: no visible global function definition for ‘var’
Undefined global functions or variables:
  dgamma dmultinom gray image kmeans rgamma rnorm runif var
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "image")
  importFrom("stats", "dgamma", "dmultinom", "kmeans", "rgamma", "rnorm",
             "runif", "var")
to your NAMESPACE file.
Call with DUP:
   .C(R_clusterer, E = as.double(E), X = as.double(X), W = as.double(W), 
       P = as.double(P), y = as.double(y), prob = as.double(prob), 
       theta = as.double(theta), lambda = as.double(lambda * n), 
       n = as.integer(n), g = as.integer(g), m = as.integer(m), 
       p = as.integer(p), critflag = as.integer(critflag), penflag = as.integer(penflag), 
       blockflag = as.integer(blockflag), valiflag = as.integer(valiflag), 
       traceflag = as.integer(trace), genliste = integer(lSize), 
       kriterium = double(lSize), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘supclust/libs/supclust.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package which this enhances but not available for checking: ‘gputools’
HCLtree: no visible global function definition for ‘hclust’
HCLtree: no visible global function definition for ‘as.dist’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matplot’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘matlines’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘axis’
plotProfilesAcrossAllSamples: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matplot’
plotProfilesWithinBicluster: no visible global function definition for
  ‘title’
plotProfilesWithinBicluster: no visible global function definition for
  ‘axis’
plotProfilesWithinBicluster: no visible global function definition for
  ‘par’
plotProfilesWithinBicluster: no visible global function definition for
  ‘box’
plotProfilesWithinBicluster: no visible global function definition for
  ‘matlines’
plotProfilesWithinBicluster: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  as.dist axis box hclust legend matlines matplot par title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "matlines", "matplot",
             "par", "title")
  importFrom("stats", "as.dist", "hclust")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘boa’ ‘coda’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
superdiag: no visible global function definition for ‘as.mcmc.list’
superdiag: no visible global function definition for ‘as.mcmc’
superdiag: no visible global function definition for ‘runif’
superdiag: no visible global function definition for ‘geweke.diag’
superdiag: no visible global function definition for ‘heidel.diag’
superdiag: no visible global function definition for ‘raftery.diag’
superdiag: no visible global function definition for ‘gelman.diag’
Undefined global functions or variables:
  as.mcmc as.mcmc.list gelman.diag geweke.diag heidel.diag raftery.diag
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
'::' or ':::' import not declared from: ‘doMC’
TrainSuperMDS: no visible global function definition for ‘rnorm’
TrainSuperMDSOnce: no visible global function definition for ‘cmdscale’
TrainSuperMDSOnce: no visible global function definition for ‘quantile’
distmat: no visible global function definition for ‘dist’
Undefined global functions or variables:
  cmdscale dist quantile rnorm
Consider adding
  importFrom("stats", "cmdscale", "dist", "quantile", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/SuppDists.Rcheck/00install.out’ for details.
File ‘SuppDists/libs/SuppDists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Found the following apparent S3 methods exported but not registered:
  print.SurvAM
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Est.Var.CCH.trueweights: no visible binding for global variable ‘var’
getEstimatesSP: no visible global function definition for ‘quantile’
getEstimatesSP: no visible global function definition for ‘resid’
prepareDataNP: no visible global function definition for
  ‘complete.cases’
prepareDataSP: no visible global function definition for
  ‘complete.cases’
processRawOutput: no visible global function definition for ‘qnorm’
survAM.estimate: no visible global function definition for ‘median’
survAM.estimate: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  complete.cases median qnorm quantile resid sd var
Consider adding
  importFrom("stats", "complete.cases", "median", "qnorm", "quantile",
             "resid", "sd", "var")
to your NAMESPACE file.
File ‘survAccuracyMeasures/libs/survAccuracyMeasures.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0

plot.survAUC: no visible global function definition for ‘plot’
plot.survAUC: no visible global function definition for ‘lines’
plot.survErr: no visible global function definition for ‘plot’
plot.survErr: no visible global function definition for ‘lines’
schemper: no visible global function definition for ‘predict’
schemper: no visible global function definition for ‘survfit’
schemper: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx lines plot predict survfit
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "predict")
to your NAMESPACE file.
File ‘survAUC/libs/survAUC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Est.PH: no visible global function definition for ‘coxph’
Inf.Cval: no visible global function definition for ‘rexp’
Inf.Cval: no visible global function definition for ‘var’
Inf.Cval.Delta: no visible global function definition for ‘rexp’
Inf.Cval.Delta: no visible global function definition for ‘var’
cvC: no visible global function definition for ‘coxph’
cvC: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  coxph rexp var weighted.mean
Consider adding
  importFrom("stats", "rexp", "var", "weighted.mean")
to your NAMESPACE file.
File ‘survC1/libs/survC1.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/survClip.Rnw’
(Is a VignetteBuilder field missing?)
pearson: no visible global function definition for ‘cor’
plot.survcorr: no visible global function definition for ‘pnorm’
plot.survcorr: no visible global function definition for ‘par’
plot.survcorr: no visible global function definition for ‘plot’
plot.survcorr: no visible global function definition for ‘points’
survcorr: no visible global function definition for ‘model.frame’
survcorr: no visible global function definition for ‘qnorm’
survcorr: no visible global function definition for ‘runif’
survcorr: no visible global function definition for ‘pnorm’
survcorr: no visible global function definition for ‘var’
survcorr: no visible global function definition for ‘qt’
Undefined global functions or variables:
  cor model.frame par plot pnorm points qnorm qt runif var
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "cor", "model.frame", "pnorm", "qnorm", "qt",
             "runif", "var")
to your NAMESPACE file.
File ‘surveybootstrap/libs/surveybootstrap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘survival’ which was already attached by Depends.
  Please remove these calls from your code.
Survgini: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  pchisq
Consider adding
  importFrom("stats", "pchisq")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘survC1’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Est.HR.FUN: no visible global function definition for ‘coxph’
Est.HR.FUN: no visible global function definition for ‘basehaz’
Est.HR.FUN: no visible global function definition for ‘approx’
Ghat.FUN: no visible global function definition for ‘survfit’
IDI.INF: no visible global function definition for ‘kmcens’
IDI.INF: no visible global function definition for ‘quantile’
IDI.INF.GRAPH: no visible global function definition for ‘plot’
IDI.INF.GRAPH: no visible global function definition for ‘lines’
IDI.INF.GRAPH: no visible global function definition for ‘abline’
IDI.INF.GRAPH: no visible global function definition for ‘points’
IDI.INF.GRAPH: no visible global function definition for ‘title’
PTB.IDI.FUN: no visible global function definition for ‘rexp’
shade: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  abline approx basehaz coxph kmcens lines plot points polygon quantile
  rexp survfit title
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points", "polygon",
             "title")
  importFrom("stats", "approx", "quantile", "rexp")
to your NAMESPACE file.
Rd file 'IDI.INF.GRAPH.Rd':
  \usage lines wider than 90 characters:
     IDI.INF.GRAPH(x, main = NULL, xlab = NULL, ylab = NULL, cex.main = NULL, cex.lab = NULL, ...)

Rd file 'IDI.INF.Rd':
  \usage lines wider than 90 characters:
     IDI.INF(indata, covs0, covs1, t0, npert = 300, npert.rand = NULL, seed1 = NULL, alpha = 0.05)

These lines will be truncated in the PDF manual.
File ‘survIDINRI/libs/survIDINRI.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘survivalROC/libs/survivalROC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
betaEst: no visible global function definition for ‘is’
fullKernel: no visible global function definition for ‘is’
halfKernel: no visible global function definition for ‘is’
kernelAuto: no visible global function definition for ‘quantile’
kernelAuto: no visible global function definition for ‘lm’
kernelAuto: no visible global function definition for ‘pnorm’
kernelFixed: no visible global function definition for ‘pnorm’
lastValue: no visible global function definition for ‘pnorm’
nearValue: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  is lm pnorm quantile
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "lm", "pnorm", "quantile")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running examples in ‘SurvRank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CVrankSurv_fct
> ### Title: Main function of SurvRank.
> ### Aliases: CVrankSurv_fct
> ### Keywords: SurvRank
> 
> ### ** Examples
> 
> ## Simulating a survival data set
> N=100; p=10; n=4
> x=data.frame(matrix(rnorm(N*p),nrow=N,p))
> beta=rnorm(n)
> mx=matrix(rnorm(N*n),N,n)
> fx=mx[,seq(n)]%*%beta/3
> hx=exp(fx)
> ty=rexp(N,hx)
> tcens=1-rbinom(n=N,prob=.3,size=1)
> y=Surv(ty,tcens)
> data=list()
> data$x<-x; data$y<-y
> ## Ranking the features according to their significance in the univariate cox models
> out.cox<-CVrankSurv_fct(data,2,3,3,fs.method="cox.rank")

  |                                                                            
  |==============                                                        |  20%Error in output[[i]][[3]] : subscript out of bounds
Calls: CVrankSurv_fct
Execution halted
File ‘survSNP/libs/survSNP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
fitModel: no visible global function definition for ‘var’
fitModel: no visible global function definition for ‘cov’
svpls: no visible global function definition for ‘pt’
Undefined global functions or variables:
  cov pt var
Consider adding
  importFrom("stats", "cov", "pt", "var")
to your NAMESPACE file.
Calls with DUP:
   .C("myInversion", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, DUP = FALSE, PACKAGE = "svcm")
   .C("myTrace", Senv$diag, Senv$env, Senv$xenv, Senv$N, Senv$Nenv, 
       Senv$Nplus1, BBenv$diag, BBenv$env, BBenv$xenv, BBenv$N, 
       BBenv$Nenv, BBenv$Nplus1, ED = ED, DUP = FALSE, PACKAGE = "svcm")
   .C("dsC2env", N, A@x, as.integer(A@i), as.integer(A@p), diagvec = diagvec, 
       env = env, xenv = as.integer(xenv), DUP = FALSE)
DUP is no longer supported and will be ignored.
File ‘svcm/libs/svcm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/svd.Rcheck/00install.out’ for details.
svd3dplot: no visible global function definition for ‘wireframe’
svd3dplot: no visible global function definition for ‘levelplot’
Undefined global functions or variables:
  levelplot wireframe
startHttpServer : <anonymous> : Rjsonp: no visible global function
  definition for ‘localeToCharset’
Undefined global functions or variables:
  localeToCharset
Consider adding
  importFrom("utils", "localeToCharset")
to your NAMESPACE file.
.onAttach : svBrowser: no visible global function definition for
  ‘browseURL’
.onAttach: no visible global function definition for ‘loadhistory’
Undefined global functions or variables:
  browseURL loadhistory
Consider adding
  importFrom("utils", "browseURL", "loadhistory")
to your NAMESPACE file.
File ‘svmadmm/libs/svmadmm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘SVMMatch/libs/SVMMatch.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘svmpath/libs/svmpath.so’:
  Found ‘_gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘_gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’
  Found ‘_gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
File ‘svmpath/libs/svmpath.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
processSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
completeCol: no visible global function definition for ‘colors’
completeCol: no visible global function definition for ‘col2rgb’
completeCol: no visible global function definition for ‘palette’
Undefined global functions or variables:
  col2rgb colors palette
Consider adding
  importFrom("grDevices", "col2rgb", "colors", "palette")
to your NAMESPACE file.
.formatResult : capture.str: no visible global function definition for
  ‘str’
createLog: no visible global function definition for ‘sessionInfo’
protocol_junit.svSuiteData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svSuiteData: no visible global function definition for
  ‘addChildren’
protocol_junit.svSuiteData: no visible global function definition for
  ‘saveXML’
protocol_junit.svTestData: no visible global function definition for
  ‘xmlNode’
protocol_junit.svTestData: no visible global function definition for
  ‘addChildren’
Undefined global functions or variables:
  addChildren saveXML sessionInfo str xmlNode
Consider adding
  importFrom("utils", "sessionInfo", "str")
to your NAMESPACE file.
svycox.calibrate: no visible global function definition for ‘quantile’
svycox.calibrate: no visible binding for global variable ‘median’
svycox.calibrate: no visible global function definition for
  ‘as.formula’
svycox.calibrate: no visible global function definition for ‘plot’
svycox.calibrate: no visible global function definition for ‘arrows’
svycox.calibrate: no visible global function definition for ‘abline’
svycox.nomogram: no visible global function definition for ‘predict’
svycox.nomogram: no visible global function definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘as.formula’
svycox.validate : internal.validate.func: no visible global function
  definition for ‘formula’
Undefined global functions or variables:
  abline arrows as.formula formula median plot predict quantile
Consider adding
  importFrom("graphics", "abline", "arrows", "plot")
  importFrom("stats", "as.formula", "formula", "median", "predict",
             "quantile")
to your NAMESPACE file.
additional_comp: no visible global function definition for ‘aggregate’
additional_compPV : <anonymous>: no visible global function definition
  for ‘aggregate’
cor.aux.func : <anonymous>: no visible global function definition for
  ‘cov.wt’
eta.func : <anonymous>: no visible global function definition for ‘lm’
eta.func : <anonymous>: no visible global function definition for
  ‘anova’
glm.dummy.no.std: no visible global function definition for
  ‘as.formula’
pv_by: no visible binding for global variable ‘var’
pv_perc: no visible binding for global variable ‘var’
pv_quantile: no visible binding for global variable ‘var’
svyPVcor: no visible global function definition for ‘update’
svyPVcor: no visible global function definition for ‘var’
svyPVeta: no visible global function definition for ‘update’
svyPVeta: no visible global function definition for ‘var’
svyPVglm: no visible global function definition for ‘gaussian’
svyPVglm: no visible binding for global variable ‘as.formula’
svyPVglm: no visible binding for global variable ‘var’
svyPVglm: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘as.formula’
svyPVttest: no visible global function definition for ‘var’
svyPVttest: no visible global function definition for ‘pt’
svyPVttest: no visible binding for global variable ‘var’
t.test.aux: no visible global function definition for ‘as.formula’
t.test.aux: no visible global function definition for ‘complete.cases’
Undefined global functions or variables:
  aggregate anova as.formula complete.cases cov.wt gaussian lm pt
  update var
Consider adding
  importFrom("stats", "aggregate", "anova", "as.formula",
             "complete.cases", "cov.wt", "gaussian", "lm", "pt",
             "update", "var")
to your NAMESPACE file.
readSWAT: no visible global function definition for ‘read.fortran’
runSWAT2005: no visible global function definition for ‘read.fortran’
runSWAT2009: no visible global function definition for ‘read.fortran’
runSWAT2012: no visible global function definition for ‘read.fortran’
Undefined global functions or variables:
  read.fortran
Consider adding
  importFrom("utils", "read.fortran")
to your NAMESPACE file.
Rd file 'build_swat_basic.Rd':
  \examples lines wider than 100 characters:
     build_swat_basic(dirname="test", iyr="1979", nbyr=13, wsarea=40, elev=200, declat=45, declon=-72, hist_wx=hist_wx) 

Rd file 'readSWAT.Rd':
  \examples lines wider than 100 characters:
       } else { print ("You need to add your file type to this function if it is not output.sub or output.rch")}

These lines will be truncated in the PDF manual.
Found the following Makefile(s) with an include directive with a pathname using R_HOME:
  src/Makefile.win
  src/SWAT2005/Makefile
  src/SWAT2005/Makefile.win
  src/SWAT2009/Makefile
  src/SWAT2009/Makefile.win
  src/SWAT2012/Makefile
  src/SWAT2012/Makefile.win
Even though not recommended, variable R_HOME may contain spaces.
Makefile directives use space as a separator and there is no portable
way to quote/escape the space in Make rules and directives.  However,
one can and should quote pathnames when passed from Makefile to the
shell, and this can be done specifically when invoking Make recursively.
It is therefore recommended to use the Make '-f' option to include files
in directories specified using R_HOME.  This option can be specified
multiple times to include multiple Makefiles.  Note that 'Makeconf' is
included automatically into top-level makefile of a package.
More information can be found in 'Writing R Extensions'.
'::' or ':::' import not declared from: ‘fracdiff’
Packages in Depends field not imported from:
  ‘MASS’ ‘fda’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fj_pl: no visible global function definition for ‘getbasismatrix’
fj_pl: no visible global function definition for ‘create.bspline.basis’
fj_pl: no visible global function definition for ‘getbasispenalty’
forward_backward.quantities : <anonymous>: no visible global function
  definition for ‘dnorm’
function_cases1AND2: no visible global function definition for ‘dnorm’
function_cases3AND4: no visible global function definition for ‘dnorm’
pij_iid: no visible global function definition for ‘dnorm’
pilj: no visible global function definition for ‘dnorm’
updateLambda: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  create.bspline.basis dnorm getbasismatrix getbasispenalty optimize
Consider adding
  importFrom("stats", "dnorm", "optimize")
to your NAMESPACE file.
calc_MW: no visible global function definition for ‘read.table’
cfba_moment: no visible global function definition for ‘median’
cfba_moment: no visible global function definition for ‘write.csv’
cfba_moment_mr: no visible global function definition for ‘median’
cfba_moment_mr: no visible global function definition for ‘write.csv’
cfba_moment_pw: no visible global function definition for ‘median’
cfba_moment_pw: no visible global function definition for ‘write.csv’
readmodel: no visible global function definition for ‘as’
Undefined global functions or variables:
  as median read.table write.csv
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "median")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking: ‘sylly.de’ ‘sylly.es’
symbol: no visible global function definition for ‘plot.new’
symbol: no visible global function definition for ‘plot.window’
symbol: no visible global function definition for ‘axis’
symbol: no visible global function definition for ‘box’
symbol: no visible global function definition for ‘title’
symbol: no visible global function definition for ‘rainbow’
symbol: no visible global function definition for ‘hsv’
symbol: no visible global function definition for ‘rect’
symbol: no visible global function definition for ‘polygon’
symbol: no visible global function definition for ‘lines’
symbol: no visible global function definition for ‘text’
Undefined global functions or variables:
  axis box hsv lines plot.new plot.window polygon rainbow rect text
  title
Consider adding
  importFrom("grDevices", "hsv", "rainbow")
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "polygon", "rect", "text", "title")
to your NAMESPACE file.
Rd file 'symbol.Rd':
  \usage lines wider than 90 characters:
     symbol(df, type="star", colin=NULL, colout=NULL, colin2=NA, colout2=1, ssize=NULL, labels=0, labelsize=0.6,
            scheme=1, sortby=0, descending=FALSE, coorx=NULL, coory=NULL, lty=1, main=NULL, sub=NULL, xlab=NULL, ylab=NULL,
            add=FALSE, xlim=NULL, ylim=NULL, facew=0.5, faceh=0.5, eyes=0.5, eyed=0.5, mouthw=0.5, mouthc=0.5, brows=0.5,
            browp=0.5, nosel=0.5, nosew=0.5, ears=0.5, pupils=0.5, body=0.5, limb1=0.5, limb2=0.5, limb3=0.5, limb4=0.5, defcol=NA)

These lines will be truncated in the PDF manual.
integrate.polynomial : f: no visible global function definition for
  ‘dmvnorm’
Undefined global functions or variables:
  dmvnorm
Package in Depends field not imported from: ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cwt_fw: no visible global function definition for ‘fft’
cwt_iw: no visible global function definition for ‘fft’
est_riskshrink_thresh: no visible global function definition for
  ‘median’
Undefined global functions or variables:
  fft median
Consider adding
  importFrom("stats", "fft", "median")
to your NAMESPACE file.
File ‘SynchWave/libs/SynchWave.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
Namespaces with empty importFrom:
  ‘Rcpp’ ‘methods’
File ‘synlik/libs/synlik.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
mainNetFunction: no visible global function definition for ‘png’
mainNetFunction: no visible global function definition for ‘plot’
mainNetFunction: no visible global function definition for ‘lines’
mainNetFunction: no visible global function definition for ‘legend’
mainNetFunction: no visible global function definition for ‘dev.off’
plotPR: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘plot’
plotROC: no visible global function definition for ‘lines’
simulatedData: no visible global function definition for ‘rpois’
simulatedData : <anonymous>: no visible global function definition for
  ‘rpois’
simulatedData : rlognormpois: no visible global function definition for
  ‘rnorm’
simulatedData : rlognormpois: no visible global function definition for
  ‘rpois’
Undefined global functions or variables:
  dev.off legend lines plot png rnorm rpois
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "rnorm", "rpois")
to your NAMESPACE file.
'data(package=)' call not declared from: ‘ggplot2’
'library' or 'require' calls in package code:
  ‘LowRankQP’ ‘rgenoud’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
fn.V: no visible global function definition for ‘LowRankQP’
gaps.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘lines’
path.plot: no visible global function definition for ‘abline’
path.plot: no visible global function definition for ‘legend’
synth: no visible binding for global variable ‘sd’
synth: no visible binding for global variable ‘var’
synth: no visible global function definition for ‘LowRankQP’
Undefined global functions or variables:
  LowRankQP abline legend lines sd var
Consider adding
  importFrom("graphics", "abline", "legend", "lines")
  importFrom("stats", "sd", "var")
to your NAMESPACE file.
Found the following significant warnings:
  lib_FeasibleMatrix.cpp:53:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:168:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_FeasibleMatrix.cpp:176:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  lib_sample_kcycle.cpp:141:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/systemicrisk.Rcheck/00install.out’ for details.
.checkDimAndTest: no visible global function definition for
  ‘chisq.test’
.checkDimAndTest: no visible global function definition for
  ‘fisher.test’
plotTable1Heatmap: no visible global function definition for ‘par’
plotTable1Heatmap: no visible global function definition for ‘image’
plotTable1Heatmap: no visible global function definition for ‘abline’
plotTable1Heatmap: no visible global function definition for ‘axis’
plotTable1Heatmap: no visible global function definition for ‘text’
plotTable1Heatmap: no visible global function definition for ‘legend’
plotTable1Heatmap: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box chisq.test fisher.test image legend par text
Consider adding
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "text")
  importFrom("stats", "chisq.test", "fisher.test")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  rbind.tableList rbind.tableMatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'rbind.tableList':
  ‘rbind.tableList’

S3 methods shown with full name in documentation object 'rbind.tableMatrix':
  ‘rbind.tableMatrix’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘tableMatrix-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getRow.tableMatrix
> ### Title: Get or set row from the matrix attribute
> ### Aliases: getRow.tableMatrix setRow.tableMatrix
> 
> ### ** Examples
> 
> 
> data(images8By8)
> data(images10By10)
> 
> # Create tableMatrix from images8By8 and images10By10
> TM <- tableMatrix(list(images8By8, images10By10), list(1:3, 1:3),
+ list(4:ncol(images8By8),4:ncol(images10By10)))
Error in setkeyv(obj$tab, c(tmName$matN, tmName$matRow)) : 
  x is not a data.table
Calls: tableMatrix -> setkeyv
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 63-93 (tableMatrix-Overview.Rmd) 
Error: processing vignette ‘tableMatrix-Overview.Rmd’ failed with diagnostics:
x is not a data.table
Execution halted
'library' or 'require' call to ‘grid’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' call to ‘perturb’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘grid’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cellgram: no visible global function definition for ‘grid.rect’
cellgram: no visible global function definition for ‘gpar’
cellgram: no visible global function definition for ‘grid.segments’
cellgram: no visible global function definition for ‘grid.circle’
cellgram: no visible global function definition for ‘grid.polygon’
cellgram: no visible global function definition for ‘grid.text’
cellgram: no visible global function definition for ‘unit’
compare: no visible global function definition for ‘sd’
tableplot.colldiag: no visible global function definition for
  ‘colldiag’
tableplot.colldiag: no visible global function definition for ‘xtabs’
tableplot.default: no visible global function definition for
  ‘grid.newpage’
tableplot.default: no visible global function definition for
  ‘grid.layout’
tableplot.default: no visible global function definition for ‘unit’
tableplot.default: no visible global function definition for
  ‘pushViewport’
tableplot.default: no visible global function definition for ‘viewport’
tableplot.default: no visible global function definition for
  ‘grid.text’
tableplot.default: no visible global function definition for
  ‘upViewport’
tableplot.default: no visible global function definition for ‘gpar’
tableplot.default: no visible global function definition for
  ‘grid.rect’
tableplot.default: no visible global function definition for
  ‘popViewport’
Undefined global functions or variables:
  colldiag gpar grid.circle grid.layout grid.newpage grid.polygon
  grid.rect grid.segments grid.text popViewport pushViewport sd unit
  upViewport viewport xtabs
Consider adding
  importFrom("stats", "sd", "xtabs")
to your NAMESPACE file.
Rd file 'Linehan.Rd':
  \examples lines wider than 100 characters:
             cell.specs=list(list(0,"grey50",1,1,"red",1,"white","grey90",2,.7,"black",FALSE,"black",99)),
             cell.specs=list(list(0,c("black","blue"),1,1,c("black","blue"),1,"white","grey80",2,.7,"black",FALSE,"black",99))

Rd file 'cellgram.Rd':
  \usage lines wider than 90 characters:
     cellgram(cell, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape.lty.neg = 1, cell.fill = "whi ... [TRUNCATED]

Rd file 'congruence.array.Rd':
  \usage lines wider than 90 characters:
     congruence.array(X, FUN = congruence.coef, stat.name = "phi", round = FALSE, scale = 1, ref = "last")

Rd file 'make.specs0.Rd':
  \usage lines wider than 90 characters:
     make.specs0(n = NULL, as.data.frame = FALSE, shape = 0, shape.col = "black", shape.lty = 1, shape.neg = 0, shape.col.neg = "red", shape ... [TRUNCATED]
     cell.fill = "white", back.fill = "white", label = 0, label.size = 0.7, label.col = "black", ref.lines = FALSE, ref.col = "gray80",  sca ... [TRUNCATED]

Rd file 'tableplot.Rd':
  \usage lines wider than 90 characters:
             v.parts = 0, h.parts = 0, gap = 2, text.m = 0, empty.text.size = 0.8, empty.text.col = "grey30", 
             title = NULL, table.label = TRUE, label.size = 0.8, side.rot = 0, left.space = 10, top.space = 10+10*(!is.null(title)), ...)
  \examples lines wider than 100 characters:
             cell.specs = list(list(0,"grey50",1,0,"red",1,"white","grey80",1,0.7,"black",FALSE,"black",93)),

These lines will be truncated in the PDF manual.
Found the following apparent S3 methods exported but not registered:
  print.plist
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TCRsink: no visible global function definition for ‘head’
Undefined global functions or variables:
  head
Consider adding
  importFrom("utils", "head")
to your NAMESPACE file.
itabplot : <anonymous>: no visible global function definition for
  ‘capture.output’
itabplot: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL capture.output
Consider adding
  importFrom("utils", "browseURL", "capture.output")
to your NAMESPACE file.
File ‘tagcloud/libs/tagcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tailDepFun/libs/tailDepFun.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  proj.data proj.dir proj.dir2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
NANOVA.test: no visible global function definition for ‘ecdf’
NANOVA.test2: no visible global function definition for ‘ecdf’
NANOVA.test3: no visible global function definition for ‘ecdf’
fdr.table: no visible global function definition for ‘median’
fdr.table: no visible global function definition for ‘quantile’
gene.classifier1: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  ecdf median quantile write.table
Consider adding
  importFrom("stats", "ecdf", "median", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'NANOVA.test.Rd':
  \usage lines wider than 90 characters:
     NANOVA.test2(data,f1,f2,type,time.course,equal.size=FALSE,B=100,robustify=FALSE,eb=FALSE,df=0)

Rd file 'tanova.Rd':
  \usage lines wider than 90 characters:
     tanova(data, f1, f2, tp, B=100, FDR=0.05,robustify=FALSE, equal.size=FALSE, qt=-1, longitudinal=TRUE, test.type=0,eb=FALSE,df=0)
     gene.classifier1(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, eb=FALSE,qt=-1)
     gene.classifier2(data, f1, f2, B=100,FDR=0.05, robustify=FALSE, equal.size=FALSE, time.course, qt=-1,eb=FALSE,df=1)

These lines will be truncated in the PDF manual.
'library' or 'require' calls in package code:
  ‘gdata’ ‘ggplot2’ ‘grid’ ‘lattice’ ‘xtable’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  as.matrix.by stack.list
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘taRifx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stack.list
> ### Title: Stack lists into data.frames
> ### Aliases: stack.list
> 
> ### ** Examples
> 
> dat <- replicate(10, data.frame(x=runif(2),y=rnorm(2)), simplify=FALSE)
> str(dat)
List of 10
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.266 0.372
  ..$ y: num [1:2] 0.184 -0.836
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.945 0.661
  ..$ y: num [1:2] 0.33 -0.82
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.687 0.384
  ..$ y: num [1:2] 0.738 0.576
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.38 0.777
  ..$ y: num [1:2] 1.51 0.39
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.267 0.386
  ..$ y: num [1:2] -2.21 1.12
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.482 0.6
  ..$ y: num [1:2] -0.0162 0.9438
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.794 0.108
  ..$ y: num [1:2] 0.594 0.919
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.783 0.553
  ..$ y: num [1:2] 0.0746 -1.9894
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.732 0.693
  ..$ y: num [1:2] -0.0561 -0.1558
 $ :'data.frame':	2 obs. of  2 variables:
  ..$ x: num [1:2] 0.0707 0.0995
  ..$ y: num [1:2] -0.478 0.418
> stack(dat)
Error in stack.default(dat) : at least one vector element is required
Calls: stack -> stack.default
Execution halted
AnalyzeLVZ: no visible global function definition for ‘approx’
ConvP2Vdepthinv: no visible global function definition for ‘approx’
DistSummary: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘heat.colors’
Earthplot: no visible global function definition for ‘par’
Earthplot: no visible global function definition for ‘plot’
Earthplot: no visible global function definition for ‘approx’
Earthplot: no visible global function definition for ‘image’
Earthplot: no visible binding for global variable ‘lines’
FindRoots: no visible global function definition for ‘uniroot’
InterpModel: no visible global function definition for ‘approx’
LinInterp: no visible global function definition for ‘approx’
PolarPlot: no visible binding for global variable ‘plot’
Rayfan: no visible binding for global variable ‘lines’
polaraxis: no visible global function definition for ‘text’
Undefined global functions or variables:
  approx heat.colors image lines par plot text uniroot
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "image", "lines", "par", "plot", "text")
  importFrom("stats", "approx", "uniroot")
to your NAMESPACE file.
Rd file 'DistSummary.Rd':
  \usage lines wider than 90 characters:
     DistSummary(delta, h, model, phaselist = 'default', prop = "vp", image.col = heat.colors(500), n = 200, ...)

Rd file 'Rayfan.Rd':
  \usage lines wider than 90 characters:
     Rayfan(phaselist, h, model, deltalist = 1:17 * 20, minp = 0.5, plot = TRUE, add = TRUE, col = rep("black", length(phaselist)), verbose  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘tbart/libs/tbart.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
BootTree: no visible global function definition for ‘hclust’
BootTree: no visible global function definition for ‘dist’
BootTree: no visible global function definition for ‘as.dist’
BootTree: no visible global function definition for ‘cor’
BootTree: no visible binding for global variable ‘var’
Pgpd: no visible global function definition for ‘optim’
Pgpd : <anonymous>: no visible global function definition for ‘optim’
Pgpd: no visible global function definition for ‘var’
Pgpd: no visible global function definition for ‘rnorm’
Pgpd: no visible global function definition for ‘quantile’
Pvalue: no visible global function definition for ‘rnorm’
SigTree: no visible global function definition for ‘data’
TreeStat: no visible global function definition for ‘hclust’
TreeStat: no visible global function definition for ‘as.dist’
TreeStat: no visible global function definition for ‘dist’
TreeStat: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘hclust’
plot.best: no visible global function definition for ‘as.dist’
plot.best: no visible global function definition for ‘dist’
plot.best: no visible global function definition for ‘cor’
plot.best: no visible global function definition for ‘plot’
treetext: no visible global function definition for ‘par’
treetext: no visible global function definition for ‘text’
Undefined global functions or variables:
  as.dist cor data dist hclust optim par plot quantile rnorm text var
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "optim",
             "quantile", "rnorm", "var")
  importFrom("utils", "data")
to your NAMESPACE file.
Running examples in ‘TCGAretriever-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: expand_cases
> ### Title: Explode TCGA Case Identifiers from a TCGA Study
> ### Aliases: expand_cases
> 
> ### ** Examples
> 
> expand_cases("blca_tcga")
Error in all_cases[i, 5] : subscript out of bounds
Calls: expand_cases -> lapply -> FUN
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: sn
Loading required package: stats4

Attaching package: 'sn'

The following object is masked from 'package:stats':

    sd

Loading required package: mclust
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: cluster
Warning in .tkmeans.warn(O, ret) :
  Clusters with size < n * 0.02 found - try reducing k.
Warning in .tclust.warn(O, O$ret) :
  The result is artificially constrained due to restr.fact = 12.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘tclust.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following apparent S3 methods exported but not registered:
  slice.fun
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'top.fun':
  ‘slice.fun’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘tcR/libs/tcR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cluster_cutoff_at_first_empty_bin: no visible global function
  definition for ‘hist’
mapper1D: no visible global function definition for ‘dist’
mapper1D: no visible global function definition for ‘as.dist’
mapper1D: no visible global function definition for ‘hclust’
mapper1D: no visible global function definition for ‘cutree’
mapper2D: no visible global function definition for ‘dist’
mapper2D: no visible global function definition for ‘as.dist’
mapper2D: no visible global function definition for ‘hclust’
mapper2D: no visible global function definition for ‘cutree’
Undefined global functions or variables:
  as.dist cutree dist hclust hist
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "as.dist", "cutree", "dist", "hclust")
to your NAMESPACE file.
File ‘TDboost/libs/TDboost.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘RSEIS’ ‘pracma’ ‘signal’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
tdt.quad: no visible global function definition for ‘runif’
tdt.rr: no visible global function definition for ‘pf’
tdt.rr: no visible global function definition for ‘qbeta’
Undefined global functions or variables:
  pf qbeta runif
Consider adding
  importFrom("stats", "pf", "qbeta", "runif")
to your NAMESPACE file.
File ‘tdthap/libs/tdthap.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
E.2SI: no visible binding for global variable ‘var’
E.2SI: no visible global function definition for ‘var’
E.BE: no visible global function definition for ‘var’
E.Beta: no visible global function definition for ‘var’
E.PO: no visible global function definition for ‘var’
E.PPS: no visible global function definition for ‘var’
E.SI: no visible global function definition for ‘var’
E.STPPS: no visible global function definition for ‘var’
E.STSI: no visible global function definition for ‘var’
E.STpiPS: no visible global function definition for ‘var’
E.SY: no visible global function definition for ‘var’
E.WR: no visible global function definition for ‘var’
E.piPS: no visible global function definition for ‘var’
GREG.SI: no visible global function definition for ‘var’
S.BE: no visible global function definition for ‘runif’
S.PO: no visible global function definition for ‘runif’
S.PPS: no visible global function definition for ‘runif’
S.SI: no visible global function definition for ‘runif’
S.STPPS: no visible global function definition for ‘runif’
S.WR: no visible global function definition for ‘rbinom’
S.piPS: no visible global function definition for ‘runif’
p.WR: no visible global function definition for ‘dmultinom’
Undefined global functions or variables:
  dmultinom rbinom runif var
Consider adding
  importFrom("stats", "dmultinom", "rbinom", "runif", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.Weights predict.Weights2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
TeachNet: no visible global function definition for ‘predict’
createWeights1: no visible global function definition for ‘rnorm’
createWeights2: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rnorm
Consider adding
  importFrom("stats", "predict", "rnorm")
to your NAMESPACE file.
aniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  $.tensor ^.tensor as.contravariate.character as.covariate.character
  as.tensor.default as.tensor.tensor is.contravariate.character
  is.contravariate.numeric is.contravariate.tensor
  is.covariate.character is.covariate.numeric is.covariate.tensor
  mean.tensor |.tensor
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Calls with DUP:
   .C(tensoraCmulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.complex(X[xtidx]), as.complex(Y[ytidx]), 
       erg = complex(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
   .C(tensoramulhelper, dimx = as.integer(c(outerx, inner, para)), 
       as.integer(c(inner, outery, para)), as.integer(c(outerx, 
           outery, para)), as.numeric(X[xtidx]), as.numeric(Y[ytidx]), 
       erg = numeric(outerx * outery * para), NAOK = TRUE, DUP = FALSE)
DUP is no longer supported and will be ignored.
S3 methods shown with full name in documentation object 'mean.tensor':
  ‘mean.tensor’

S3 methods shown with full name in documentation object 'solve.tensor':
  ‘solve.tensor’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘tensorA/libs/tensorA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘tensorA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.tensor
> ### Title: Coercion to a tensor
> ### Aliases: as.tensor as.tensor.default as.tensor.tensor
> ### Keywords: arith
> 
> ### ** Examples
> 
> A <- diag(5)
> as.tensor(A)
Error in UseMethod("as.tensor") : 
  no applicable method for 'as.tensor' applied to an object of class "c('matrix', 'double', 'numeric')"
Calls: as.tensor
Execution halted
TER.deesc.1.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B : A2.n.f: no visible binding for global variable ‘ID’
TER.deesc.1.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.1.B: no visible binding for global variable ‘ID’
TER.deesc.A.B : A1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A3.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A3.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : A2.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : A2.f: no visible binding for global variable ‘ID’
TER.deesc.A.B : B1.f: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B : B1.f: no visible binding for global variable ‘ID’
TER.deesc.A.B: no visible binding for '<<-' assignment to ‘ID’
TER.deesc.A.B: no visible binding for global variable ‘ID’
Undefined global functions or variables:
  ID
Found the following apparent S3 methods exported but not registered:
  plot.df_curves plot.dyntermstrc_nss plot.dyntermstrc_param
  plot.dyntermstrc_yields plot.error plot.fwr_curves plot.ir_curve
  plot.s_curves plot.spot_curves plot.spsearch plot.termstrc_cs
  plot.termstrc_nss plot.zeroyields print.couponbonds
  print.dyncouponbonds print.dyntermstrc_nss print.dyntermstrc_yields
  print.summary.dyntermstrc_nss print.summary.dyntermstrc_param
  print.summary.dyntermstrc_yields print.summary.termstrc_cs
  print.summary.termstrc_nss print.termstrc_cs print.termstrc_nss
  print.zeroyields summary.dyntermstrc_nss summary.dyntermstrc_param
  summary.dyntermstrc_yields summary.termstrc_cs summary.termstrc_nss
  summary.zeroyields
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘termstrc/libs/termstrc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Depends: includes the non-default packages:
  ‘grid’ ‘quadprog’ ‘maps’ ‘maptools’ ‘mapdata’ ‘dichromat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘dichromat’ ‘grid’ ‘mapdata’ ‘maps’ ‘maptools’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.tverify tverify.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ternvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: foot
> ### Title: Football betting dataset
> ### Aliases: foot
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(foot)
> # see the distribution of forecasts
> tplot(foot$p,main="Bookmaker forecasts of \n football matches",
+       dimnames=c("Home Win","Draw","Away Win"))
>       
> # see how well forecasts compare with results
> # create object of class tverify
> foot.verify <- tverify(p=foot$p,o=foot$o) 
Error in UseMethod("tverify") : 
  no applicable method for 'tverify' applied to an object of class "c('matrix', 'double', 'numeric')"
Calls: tverify
Execution halted
File ‘TESS/libs/TESS.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘testforDEP/libs/testforDEP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File which contains pragma(s) suppressing diagnostics:
  ‘inst/include/testthat/vendor/catch.h’
Found the following apparent S3 methods exported but not registered:
  print.tepAssign print.tepBADA print.tepDICA print.tepGPLS
  print.tepGraphs print.tepPLS print.tepPLSCA print.texpoOutput
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
phyper_right: no visible global function definition for ‘dhyper’
progression: no visible global function definition for ‘density’
progression: no visible global function definition for ‘plot’
progression: no visible global function definition for ‘points’
progression: no visible global function definition for ‘legend’
progression: no visible global function definition for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘dhyper’
specificities.distribution.plot: no visible global function definition
  for ‘plot’
specificities.distribution.plot: no visible global function definition
  for ‘Axis’
specificities.distribution.plot: no visible global function definition
  for ‘arrows’
specificities.distribution.plot: no visible global function definition
  for ‘text’
specificities.distribution.plot: no visible global function definition
  for ‘title’
specificities.probabilities.vector: no visible global function
  definition for ‘phyper’
Undefined global functions or variables:
  Axis arrows density dhyper legend phyper plot points text title
Consider adding
  importFrom("graphics", "Axis", "arrows", "legend", "plot", "points",
             "text", "title")
  importFrom("stats", "density", "dhyper", "phyper")
to your NAMESPACE file.
File ‘textreg/libs/textreg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘textreuse/libs/textreuse.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
.dea_create_model: no visible global function definition for
  ‘getSrcFilename’
.wMean: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
transfer: no visible global function definition for ‘rgamma’
transfer: no visible global function definition for ‘rnorm’
transfer: no visible global function definition for ‘rnbinom’
transfer: no visible global function definition for ‘rpois’
transfer: no visible global function definition for ‘rbinom’
transfer: no visible global function definition for ‘runif’
plot,transfer: no visible global function definition for ‘barplot’
plot,transfer: no visible global function definition for ‘axis’
plot,transfer: no visible global function definition for ‘par’
plot,transfer: no visible global function definition for ‘hist’
Undefined global functions or variables:
  axis barplot hist par rbinom rgamma rnbinom rnorm rpois runif
Consider adding
  importFrom("graphics", "axis", "barplot", "hist", "par")
  importFrom("stats", "rbinom", "rgamma", "rnbinom", "rnorm", "rpois",
             "runif")
to your NAMESPACE file.
ParseTrueFX: no visible global function definition for ‘read.csv’
TrueFXRef: no visible global function definition for ‘download.file’
TrueFXRef: no visible global function definition for ‘browseURL’
Undefined global functions or variables:
  browseURL download.file read.csv
Consider adding
  importFrom("utils", "browseURL", "download.file", "read.csv")
to your NAMESPACE file.
File ‘tgcd/libs/tgcd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tgp/libs/tgp.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘dada2’
Thinknum: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘ThreeArmedTrials/libs/ThreeArmedTrials.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
coef_traceplot: no visible global function definition for ‘rainbow’
coef_traceplot: no visible global function definition for ‘plot’
coef_traceplot: no visible global function definition for ‘abline’
coef_traceplot : <anonymous>: no visible global function definition for
  ‘lines’
coef_traceplot: no visible global function definition for ‘text’
ee.GEE.aux : <anonymous>: no visible global function definition for
  ‘combn’
Undefined global functions or variables:
  abline combn lines plot rainbow text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
summary.tsls: no visible global function definition for ‘printCoefmat’
threesls: no visible global function definition for ‘cor’
threesls: no visible global function definition for ‘pt’
tsls.formula: no visible global function definition for ‘model.matrix’
tsls.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  cor model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.matrix", "model.response",
             "printCoefmat", "pt")
to your NAMESPACE file.
.LoadTickDataHK: no visible global function definition for ‘read.csv’
.LoadTickDataSHSZ: no visible global function definition for ‘read.csv’
DrawDown: no visible global function definition for ‘na.omit’
PerformanceReport: no visible global function definition for
  ‘aggregate’
PerformanceReport: no visible global function definition for ‘sd’
Undefined global functions or variables:
  aggregate na.omit read.csv sd
Consider adding
  importFrom("stats", "aggregate", "na.omit", "sd")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
newTiddler: no visible global function definition for ‘new’
twImage: no visible global function definition for ‘new’
twLink: no visible global function definition for ‘new’
twList: no visible global function definition for ‘new’
twTable: no visible global function definition for ‘new’
Undefined global functions or variables:
  new
Consider adding
  importFrom("methods", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
'::' or ':::' import not declared from: ‘data.table’
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tiff/libs/tiff.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.tight.clust
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tight.clust: no visible global function definition for ‘hclust’
plot.tight.clust: no visible global function definition for ‘dist’
plot.tight.clust: no visible global function definition for ‘image’
plot.tight.clust: no visible global function definition for
  ‘colorRampPalette’
plot.tight.clust: no visible global function definition for ‘axis’
plot.tight.clust: no visible global function definition for ‘lines’
tight.clust : find.candidates : kmeans.classify: no visible global
  function definition for ‘kmeans’
write.tight.clust: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  axis colorRampPalette dist hclust image kmeans lines write.table
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "axis", "image", "lines")
  importFrom("stats", "dist", "hclust", "kmeans")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Rd file 'tight.clust.Rd':
  \usage lines wider than 90 characters:
     tight.clust(x, target, k.min, alpha = 0.1, beta = 0.6, top.can = 7, seq.num = 2, resamp.num = 10, samp.p = 0.7, nstart = 1, remain.p =  ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running examples in ‘tightClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tight.clust
> ### Title: Tight Clustering
> ### Aliases: tight.clust
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## load the test dataset
> data(tclust.test.data)
> ## find 10 tight clusters
> ptm<-proc.time()
> ## k.min=25, tighter clusters will be found
> ## target=1 is used to save time, target=10 is recommended
> tclust1<-tight.clust(tclust.test.data$Data, target=1, k.min=25, random.seed=12345)
Number of points: 1100 	Dimension: 75 

Looking for tight cluster 1 ...
k = 25
k = 26
1 tight cluster(s) found!
Cluster size: 43 	Remaining number of points: 1057 

> proc.time()-ptm
   user  system elapsed 
  3.902   0.111   5.523 
> ## plot the heat map of cluster result
> plot(tclust1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
'::' or ':::' import not declared from: ‘scales’
'library' or 'require' call not declared from: ‘lattice’
'library' or 'require' call to ‘shiny’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘ggplot2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
timeline: no visible global function definition for ‘ggplot’
timeline: no visible global function definition for ‘geom_segment’
timeline: no visible global function definition for ‘aes_string’
timeline: no visible global function definition for ‘geom_rect’
timeline: no visible global function definition for ‘geom_text’
timeline: no visible global function definition for ‘theme’
timeline: no visible global function definition for ‘element_blank’
timeline: no visible global function definition for ‘xlab’
timeline: no visible global function definition for ‘ylab’
timeline: no visible global function definition for ‘xlim’
timeline: no visible global function definition for
  ‘scale_y_continuous’
timeline: no visible global function definition for ‘geom_point’
timeline: no visible global function definition for ‘scale_color_grey’
timeline: no visible global function definition for ‘geom_hline’
Undefined global functions or variables:
  aes_string element_blank geom_hline geom_point geom_rect geom_segment
  geom_text ggplot scale_color_grey scale_y_continuous theme xlab xlim
  ylab
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/TimeMachine.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  density.tm mean.tm print.tm quantile.tm summary.tm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
density.tm: no visible global function definition for ‘density’
mu.mle: no visible global function definition for ‘optimize’
pophistory.tm: no visible binding for global variable ‘quantile’
quantile.tm: no visible global function definition for ‘quantile’
sample.pop: no visible global function definition for ‘runif’
summary.tm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  density optimize quantile runif
Consider adding
  importFrom("stats", "density", "optimize", "quantile", "runif")
to your NAMESPACE file.
File ‘TimeMachine/libs/TimeMachine.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pophistory
> ### Title: History of Population Size
> ### Aliases: pophistory pophistory.tm
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> 
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> n <- 10
> mu <- 1
> samples <- 10
> est.res <- tm(transitions, pi, pdm$population, n, mu, samples)
> 
> # Plot minimum, median and maximum SEN as a function of population size
> h <- pophistory(est.res, probs=c(0, 0.5, 1))
Error in UseMethod("pophistory") : 
  no applicable method for 'pophistory' applied to an object of class "tm"
Calls: pophistory -> pophistory
Execution halted
generatelatencies: no visible binding for global variable ‘allNames’
generatetimedeltas: no visible global function definition for ‘head’
generatetimedeltas: no visible global function definition for ‘tail’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘head’
generatevertexedgelist : <anonymous>: no visible global function
  definition for ‘tail’
plotnetworkslices: no visible global function definition for ‘par’
plotnetworkslices: no visible global function definition for ‘text’
plottanet: no visible global function definition for ‘plot’
plottonet: no visible global function definition for ‘plot’
shortesttimepath : <anonymous>: no visible global function definition
  for ‘tail’
Undefined global functions or variables:
  allNames head par plot tail text
Consider adding
  importFrom("graphics", "par", "plot", "text")
  importFrom("methods", "allNames")
  importFrom("utils", "head", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
'library' or 'require' calls in package code:
  ‘ggplot2’ ‘plyr’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Matrix’ ‘lubridate’ ‘timeDate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
is.Bizday: no visible global function definition for ‘isWeekday’
plotCalendarHeatmap: no visible global function definition for ‘ddply’
plotCalendarHeatmap: no visible global function definition for ‘.’
plotCalendarHeatmap: no visible binding for global variable ‘year’
plotCalendarHeatmap: no visible binding for global variable ‘month’
plotCalendarHeatmap: no visible binding for global variable ‘week’
plotCalendarHeatmap: no visible global function definition for ‘ggplot’
plotCalendarHeatmap: no visible global function definition for ‘aes’
plotCalendarHeatmap: no visible binding for global variable ‘monthweek’
plotCalendarHeatmap: no visible binding for global variable ‘weekday’
plotCalendarHeatmap: no visible global function definition for
  ‘geom_tile’
plotCalendarHeatmap: no visible global function definition for
  ‘facet_grid’
plotCalendarHeatmap: no visible global function definition for
  ‘scale_fill_gradientn’
projectDate: no visible global function definition for ‘holidayNYSE’
projectDate: no visible global function definition for
  ‘sparse.model.matrix’
Undefined global functions or variables:
  . aes ddply facet_grid geom_tile ggplot holidayNYSE isWeekday month
  monthweek scale_fill_gradientn sparse.model.matrix week weekday year
boot_autocov: no visible global function definition for ‘is.ts’
boot_autocov: no visible global function definition for ‘tsboot’
boot_autocov: no visible global function definition for ‘quantile’
boot_autocov: no visible global function definition for ‘par’
boot_autocov: no visible global function definition for ‘frequency’
boot_autocov: no visible global function definition for ‘polygon’
boot_autocov: no visible global function definition for ‘lines’
boot_autocov: no visible global function definition for ‘abline’
boot_autocov: no visible global function definition for ‘acf’
boot_spec: no visible global function definition for ‘is.ts’
boot_spec: no visible global function definition for ‘tsboot’
boot_spec: no visible global function definition for ‘spec.pgram’
boot_spec: no visible global function definition for ‘quantile’
boot_spec: no visible global function definition for ‘polygon’
boot_spec: no visible global function definition for ‘lines’
redraw: no visible global function definition for ‘spec.pgram’
statistic: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf frequency is.ts lines par polygon quantile spec.pgram
  tsboot
Consider adding
  importFrom("graphics", "abline", "lines", "par", "polygon")
  importFrom("stats", "acf", "frequency", "is.ts", "quantile",
             "spec.pgram")
to your NAMESPACE file.
createHstore.ts: no visible global function definition for ‘time’
exploreDb : <anonymous>: no visible global function definition for
  ‘plot’
exportTsList : <anonymous>: no visible global function definition for
  ‘time’
exportTsList: no visible global function definition for ‘write.csv2’
importTsList: no visible global function definition for ‘read.csv2’
importTsList : <anonymous>: no visible global function definition for
  ‘as.ts’
plot.tslist: no visible global function definition for ‘plot’
plot.tslist : <anonymous>: no visible global function definition for
  ‘time’
plot.tslist: no visible global function definition for ‘par’
plot.tslist: no visible global function definition for ‘legend’
readTimeSeries : <anonymous>: no visible global function definition for
  ‘ts’
resolveOverlap: no visible global function definition for ‘is.ts’
resolveOverlap: no visible global function definition for ‘frequency’
resolveOverlap: no visible global function definition for ‘time’
resolveOverlap: no visible global function definition for ‘ts’
storeTimeSeries: no visible binding for global variable ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘time’
zooLikeDateConvert: no visible global function definition for
  ‘frequency’
zooLikeDateConvert: no visible global function definition for ‘cycle’
Undefined global functions or variables:
  as.ts cycle frequency is.ts legend par plot read.csv2 time ts
  write.csv2
Consider adding
  importFrom("graphics", "legend", "par", "plot")
  importFrom("stats", "as.ts", "cycle", "frequency", "is.ts", "time",
             "ts")
  importFrom("utils", "read.csv2", "write.csv2")
to your NAMESPACE file.
'::' or ':::' imports not declared from:
  ‘fracdiff’ ‘timeDate’ ‘tseries’
author.search: no visible binding for global variable ‘na.omit’
reference.list: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘timma/libs/timma.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TIMP/libs/TIMP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘ExPosition’ ‘InPosition’ ‘TExPosition’ ‘prettyGraphs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  print.tepBADA.inference.battery print.tepDICA.inference.battery
  print.tinpoAllBoots print.tinpoBoot print.tinpoBootTests
  print.tinpoComponents print.tinpoLOO print.tinpoOmni
  print.tinpoOutput print.tinpoR2
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Non-standard files/directories found at top level:
  ‘DESCRIPTION.orig’ ‘README.rst’
tipom.car: no visible global function definition for ‘abline’
tipom.car: no visible global function definition for ‘axis’
tipom.heat: no visible global function definition for ‘image’
tipom.heat: no visible global function definition for ‘gray’
tipom.lw: no visible global function definition for ‘plot’
tipom.lw: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis gray image plot
Consider adding
  importFrom("grDevices", "gray")
  importFrom("graphics", "abline", "axis", "image", "plot")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
ls.tree: no visible global function definition for ‘lm’
ls.tree: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef lm
Consider adding
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
File ‘TKF/libs/TKF.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found an obsolete/platform-specific call in the following function:
  ‘.my.tkdev’
Found the platform-specific device:
  ‘X11’
dev.new() is the preferred way to open a new device, in the unlikely
event one is needed.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
File ‘tkrplot/libs/tkrplot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FLXmclust.Density: no visible global function definition for ‘dmvnorm’
FLXmclust.Estimate: no visible global function definition for ‘flexmix’
FLXmclust.Estimate: no visible global function definition for
  ‘FLXmclust’
coefmclust: no visible global function definition for ‘parameters’
flexmix.Density: no visible global function definition for
  ‘model.matrix’
flexmix.Density: no visible global function definition for
  ‘model.response’
flexmix.Density: no visible global function definition for
  ‘model.frame’
flexmix.Density: no visible global function definition for ‘dnorm’
flexmix.Density: no visible global function definition for ‘dpois’
flexmix.Density: no visible global function definition for ‘dbinom’
flexmix.Estimate: no visible global function definition for ‘flexmix’
flexmix.Estimate: no visible global function definition for ‘FLXglm’
tleplot,TLE-data.frame: no visible global function definition for
  ‘legend’
Undefined global functions or variables:
  FLXglm FLXmclust dbinom dmvnorm dnorm dpois flexmix legend
  model.frame model.matrix model.response parameters
Consider adding
  importFrom("graphics", "legend")
  importFrom("stats", "dbinom", "dnorm", "dpois", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
EMN: no visible global function definition for ‘dmvnorm’
EMN: no visible global function definition for ‘pmvnorm’
EMT: no visible global function definition for ‘GenzBretz’
EMT: no visible global function definition for ‘dmvt’
EMT: no visible global function definition for ‘pmvt’
MomemNT: no visible global function definition for ‘pnorm’
MomemNT: no visible global function definition for ‘dnorm’
MomemNT: no visible global function definition for ‘pmvnorm’
MomemNT: no visible global function definition for ‘dmvnorm’
TT.moment: no visible global function definition for ‘GenzBretz’
TT.moment: no visible global function definition for ‘pmvt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dmvt’
cdfNI: no visible global function definition for ‘pnorm’
cdfNI: no visible global function definition for ‘pt’
inits: no visible global function definition for ‘lm’
Undefined global functions or variables:
  GenzBretz dmvnorm dmvt dnorm dt lm pmvnorm pmvt pnorm pt
Consider adding
  importFrom("stats", "dnorm", "dt", "lm", "pnorm", "pt")
to your NAMESPACE file.
Rd file 'UTIdata.Rd':
  \examples lines wider than 100 characters:
     x = cbind((UTIdata$Fup==0)+0, (UTIdata$Fup==1)+0, (UTIdata$Fup==3)+0, (UTIdata$Fup==6)+0, (UTIdata$Fup==9)+0, (UTIdata$Fup==12)+0, (UTI ... [TRUNCATED]

These lines will be truncated in the PDF manual.
search_collection: no visible global function definition for
  ‘URLencode’
search_company: no visible global function definition for ‘URLencode’
search_keyword: no visible global function definition for ‘URLencode’
search_list: no visible global function definition for ‘URLencode’
search_movie: no visible global function definition for ‘URLencode’
search_multi: no visible global function definition for ‘URLencode’
search_person: no visible global function definition for ‘URLencode’
search_tv: no visible global function definition for ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
File ‘tmg/libs/tmg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmlenet/libs/tmlenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
extractContentDOM: no visible global function definition for
  ‘capture.output’
extractHTMLStrip: no visible global function definition for
  ‘capture.output’
Undefined global functions or variables:
  capture.output
Consider adding
  importFrom("utils", "capture.output")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘tm.lexicon.GeneralInquirer’
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tmuxr)
  > 
  > test_check("tmuxr")
  ── 1. Error: a session can be renamed (@test-session.R#28)  ────────────────────
  tmux: no current client
  1: expect_equal(rename_session(attach_session("foo"), "bar")$name, "bar") at testthat/test-session.R:28
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: rename_session(attach_session("foo"), "bar")
  5: tmux_rename_session("-t", session$name, as.character(new_name))
  6: stop(stringr::str_c("tmux: ", result, collapse = " "))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Error: a session can be renamed (@test-session.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘tmvnsim/libs/tmvnsim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tmvtnorm/libs/tmvtnorm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘corpus.JSS.papers’
File ‘TopKLists/libs/TopKLists.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Tosls.formula: no visible global function definition for ‘model.matrix’
Tosls.formula: no visible global function definition for
  ‘model.response’
summary: no visible global function definition for ‘coef’
summary: no visible global function definition for ‘pt’
Undefined global functions or variables:
  coef model.matrix model.response pt
Consider adding
  importFrom("stats", "coef", "model.matrix", "model.response", "pt")
to your NAMESPACE file.
'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package suggested but not available for checking: ‘rmongodb’
ConfA: no visible global function definition for ‘qf’
EstM2Sn: no visible global function definition for ‘nlm’
EstM2Sn: no visible global function definition for ‘qnorm’
TV.model: no visible global function definition for ‘dev.new’
TV.model: no visible global function definition for ‘points’
betaBino: no visible global function definition for ‘pbinom’
doseD: no visible global function definition for ‘lm’
doseD: no visible global function definition for ‘dev.new’
doseD: no visible global function definition for ‘par’
doseD: no visible global function definition for ‘plot’
doseD: no visible global function definition for ‘axTicks’
doseD: no visible global function definition for ‘axis’
doseD: no visible global function definition for ‘lines’
doseD: no visible global function definition for ‘abline’
doseD: no visible global function definition for ‘legend’
setD: no visible global function definition for ‘dev.new’
setD: no visible global function definition for ‘par’
setD: no visible global function definition for ‘pbinom’
setD: no visible global function definition for ‘abline’
setD: no visible global function definition for ‘axis’
setD: no visible global function definition for ‘rect’
setD: no visible global function definition for ‘lines’
setD: no visible global function definition for ‘text’
setD: no visible global function definition for ‘axTicks’
setD: no visible global function definition for ‘legend’
spoD : spoD_A: no visible global function definition for ‘chisq.test’
Undefined global functions or variables:
  abline axTicks axis chisq.test dev.new legend lines lm nlm par pbinom
  plot points qf qnorm rect text
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axTicks", "axis", "legend", "lines",
             "par", "plot", "points", "rect", "text")
  importFrom("stats", "chisq.test", "lm", "nlm", "pbinom", "qf", "qnorm")
to your NAMESPACE file.
align1d : obj: no visible global function definition for ‘dist’
align2d : obj: no visible global function definition for ‘dist’
align2d : pen: no visible global function definition for ‘dist’
align2d: no visible global function definition for ‘dist’
sumt: no visible global function definition for ‘optim’
tpe1d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘hclust’
tpe2d: no visible global function definition for ‘cmdscale’
Undefined global functions or variables:
  cmdscale dist hclust optim
Consider adding
  importFrom("stats", "cmdscale", "dist", "hclust", "optim")
to your NAMESPACE file.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/tpr.Rcheck/00install.out’ for details.
Found the following calls to attach():
File ‘track/R/track.attach.R’:
  attach(what = NULL, pos = pos, name = name)
See section ‘Good practice’ in ‘?attach’.
DeadReckoning: no visible global function definition for ‘filter’
DeadReckoning: no visible global function definition for ‘approx’
DeadReckoning: no visible global function definition for ‘lm’
Mapper: no visible global function definition for ‘colorRampPalette’
Mapper: no visible global function definition for ‘terrain.colors’
Mapper: no visible global function definition for ‘points’
Mapper: no visible global function definition for ‘axis’
Standardize: no visible global function definition for ‘lm’
Undefined global functions or variables:
  approx axis colorRampPalette filter lm points terrain.colors
Consider adding
  importFrom("grDevices", "colorRampPalette", "terrain.colors")
  importFrom("graphics", "axis", "points")
  importFrom("stats", "approx", "filter", "lm")
to your NAMESPACE file.
File ‘TransferEntropy/libs/TransferEntropy.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
microsoftTranslate: no visible global function definition for
  ‘URLencode’
Undefined global functions or variables:
  URLencode
Consider adding
  importFrom("utils", "URLencode")
to your NAMESPACE file.
Running examples in ‘translateSPSS2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: xpssFlip
> ### Title: Flips variables
> ### Aliases: xpssFlip
> 
> ### ** Examples
> 
> data(fromXPSS)
> xpssFlip(x=fromXPSS,variables=c("V4","V5","V6"),names="V1")
Error in if (variables == "all") { : the condition has length > 1
Calls: xpssFlip
Execution halted
rtrapezoid: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
File ‘trapezoid/libs/trapezoid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘treeclim/libs/treeclim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call not declared from: ‘ape’
Build_JTree: no visible global function definition for ‘flush.console’
Run_JTree: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cov2cor flush.console
Consider adding
  importFrom("stats", "cov2cor")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
LikAge: no visible global function definition for ‘read.table’
bd.ME.optim: no visible global function definition for ‘optim’
bd.ME.optim.rho: no visible global function definition for ‘optim’
bd.ME.optim.rho.all: no visible global function definition for ‘optim’
bd.MEyule.optim: no visible global function definition for ‘optimize’
bd.MEyule.optim: no visible global function definition for ‘optim’
bd.age.optim.matlab: no visible global function definition for
  ‘read.table’
bd.groups.conf: no visible global function definition for ‘uniroot’
bd.shifts.plot: no visible global function definition for ‘plot’
bd.shifts.plot: no visible global function definition for ‘lines’
bdsky.stt.optim: no visible global function definition for ‘optim’
create.mat: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  lines optim optimize plot read.table uniroot write.table
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optim", "optimize", "uniroot")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
plot.treeperm: no visible global function definition for ‘hist’
plot.treeperm: no visible global function definition for ‘points’
plot.treeperm: no visible global function definition for ‘text’
treeperm.formula: no visible global function definition for
  ‘model.frame’
treeperm.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  hist model.frame model.response points text
Consider adding
  importFrom("graphics", "hist", "points", "text")
  importFrom("stats", "model.frame", "model.response")
to your NAMESPACE file.
File ‘treeperm/libs/treeperm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls not declared from:
  ‘codetools’ ‘knitr’ ‘markdown’
File ‘TrialSize/libs/TrialSize.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘triebeard/libs/triebeard.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.trifield
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.trifield: no visible global function definition for ‘topo.colors’
plot.trifield: no visible global function definition for ‘plot’
plot.trifield: no visible global function definition for ‘image’
plot.trifield: no visible global function definition for ‘contour’
plot.trifield: no visible global function definition for ‘text’
ternary.legend: no visible global function definition for ‘arrows’
ternary.legend: no visible global function definition for ‘text’
triaxes: no visible global function definition for ‘lines’
tribox: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  arrows contour image lines plot polygon text topo.colors
Consider adding
  importFrom("grDevices", "topo.colors")
  importFrom("graphics", "arrows", "contour", "image", "lines", "plot",
             "polygon", "text")
to your NAMESPACE file.
Rd file 'plot.trifield.Rd':
  \usage lines wider than 90 characters:
     plot(x, contours = TRUE, col = topo.colors(256), lab1 = "A = 0", lab2 = "B = 0", lab3 = "C = 0", tribox = TRUE, axis.lines = TRUE, ...)

Rd file 'ternary.legend.Rd':
  \usage lines wider than 90 characters:
     ternary.legend(x0 = 0.2, y0 = 0.8, radius = 0.1, lab1 = "A", lab2 = "B", lab3 = "C", infl = 1.5, cex = 0.75, length = 0.05, ...)

These lines will be truncated in the PDF manual.
'library' or 'require' call to ‘fpc’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  plot.tkm print.tkm
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.tkm: no visible global function definition for ‘plotcluster’
plot.tkm: no visible global function definition for ‘plot’
plot.tkm: no visible global function definition for ‘points’
plot.tkm: no visible global function definition for ‘lines’
plot.tkm: no visible global function definition for ‘discrcoord’
Undefined global functions or variables:
  discrcoord lines plot plotcluster points
Consider adding
  importFrom("graphics", "lines", "plot", "points")
to your NAMESPACE file.
cinbag: no visible global function definition for ‘var’
trimTrees: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict var
Consider adding
  importFrom("stats", "predict", "var")
to your NAMESPACE file.
File ‘trimTrees/libs/trimTrees.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls to packages already attached by Depends:
  ‘gtools’ ‘mgcv’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘gtools’ ‘mgcv’ ‘msm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HtoGp: no visible global function definition for ‘odd’
HtoGp: no visible global function definition for ‘even’
plot.pirls.gam: no visible global function definition for ‘par’
plot.pirls.gam: no visible global function definition for ‘plot’
plot.pirls.gam: no visible global function definition for ‘title’
plot.pirls.gam: no visible global function definition for ‘lines’
plot.pirls.gam: no visible global function definition for ‘rug’
plot.pirls.gam: no visible global function definition for ‘mtext’
test.trioGxE: no visible global function definition for ‘write.table’
trioGxE: no visible global function definition for ‘quantile’
trioGxE: no visible global function definition for ‘qtnorm’
trioplot: no visible global function definition for ‘quantile’
trioplot: no visible global function definition for ‘formula’
trioplot: no visible global function definition for ‘gam’
trioplot: no visible global function definition for ‘binomial’
Undefined global functions or variables:
  binomial even formula gam lines mtext odd par plot qtnorm quantile
  rug title write.table
Consider adding
  importFrom("graphics", "lines", "mtext", "par", "plot", "rug", "title")
  importFrom("stats", "binomial", "formula", "quantile")
  importFrom("utils", "write.table")
to your NAMESPACE file.
File ‘tripack/libs/tripack.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in GA::ga(type = "real-valued", fitness = sofun, lfq = lfq, min = min,  :
  'min' arg is deprecated. Use 'lower' instead.
Warning in GA::ga(type = "real-valued", fitness = sofun, lfq = lfq, min = min,  :
  'max' arg is deprecated. Use 'upper' instead.
Killed
DrawMargin: no visible global function definition for ‘qnorm’
DrawProbability: no visible global function definition for ‘pnorm’
Factor: no visible global function definition for ‘new’
Gaussian: no visible global function definition for ‘new’
LikelihoodFactor: no visible global function definition for ‘new’
Parameters: no visible global function definition for ‘new’
Player: no visible global function definition for ‘new’
PriorFactor: no visible global function definition for ‘new’
SumFactor: no visible global function definition for ‘new’
TruncateFactor: no visible global function definition for ‘new’
Variable: no visible global function definition for ‘new’
Vdraw: no visible global function definition for ‘dnorm’
Vdraw: no visible global function definition for ‘pnorm’
Vwin: no visible global function definition for ‘dnorm’
Vwin: no visible global function definition for ‘pnorm’
Wdraw: no visible global function definition for ‘dnorm’
Wdraw: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm new pnorm qnorm
Consider adding
  importFrom("methods", "new")
  importFrom("stats", "dnorm", "pnorm", "qnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
cdens: no visible global function definition for ‘head’
dplot: no visible global function definition for ‘knots’
dplot: no visible global function definition for ‘median’
dplot: no visible global function definition for ‘par’
dplot: no visible global function definition for ‘plot.stepfun’
dplot: no visible global function definition for ‘abline’
edf: no visible global function definition for ‘approxfun’
mctest : rdist: no visible global function definition for ‘runif’
mctest : S: no visible global function definition for ‘optim’
qplot: no visible global function definition for ‘plot’
qplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline approxfun head knots median optim par plot plot.stepfun runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "approxfun", "knots", "median", "optim",
             "plot.stepfun", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
File ‘truncgof/libs/truncgof.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘changes’
'library' or 'require' calls to packages already attached by Depends:
  ‘leaps’ ‘locfit’ ‘mgcv’
  Please remove these calls from your code.
':::' calls which should be '::':
  ‘stats:::ARMAacf’ ‘stats:::acf’ ‘stats:::arima’
  See the note in ?`:::` about the use of this operator.
Found the following apparent S3 methods exported but not registered:
  fitted.Arima plot.Arima plot.armasubsets predict.TAR rstandard.Arima
  summary.armasubsets tsdiag.Arima tsdiag.TAR
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TSA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.Arima
> ### Title: Compute and Plot the Forecasts Based on a Fitted Time Series
> ###   Model
> ### Aliases: plot.Arima
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(oil.price)
> oil.IMA11alt=arima(log(oil.price),order=c(0,1,1),
+ # create the design matrix of the covariate for prediction
+ xreg=data.frame (constant=seq(oil.price)))
> n=length(oil.price)
> n.ahead=24
> newxreg=data.frame(constant=(n+1):(n+n.ahead))
> # do the prediction and plot the results
> plot(oil.IMA11alt,n.ahead=n.ahead,newxreg=newxreg,
+ ylab='Log(Oil Price)',xlab='Year',n1=c(2000,1))
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
dmvnb: no visible global function definition for ‘dbinom’
drvts: no visible global function definition for ‘dnorm’
drvts: no visible global function definition for ‘dbinom’
dsvts: no visible global function definition for ‘dnorm’
rescale: no visible global function definition for ‘qlogis’
rescale: no visible global function definition for ‘plogis’
tslogl: no visible global function definition for ‘dnorm’
Undefined global functions or variables:
  dbinom dnorm plogis qlogis
Consider adding
  importFrom("stats", "dbinom", "dnorm", "plogis", "qlogis")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  print.tsbugs
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'ar.bugs.Rd':
  \examples lines wider than 100 characters:
     ar2 <- ar.bugs(y = diff(LH), ar.order = 2, ar.prior = "dunif(-1,1)", var.prior = "dgamma(0.001,0.001)")

Rd file 'rv.bugs.Rd':
  \usage lines wider than 90 characters:
                     rv.tol0.prior = "dgamma(0.000001,0.000001)", rv.eps.prior = "dbeta(1, 100)", 
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

Rd file 'sv.bugs.Rd':
  \examples lines wider than 100 characters:
       plot(NULL, type = "n", xlim = tsp(sigma.pn)[1:2], ylim = range(sigma.pn[, 1:95]), main = "sigma_t")

These lines will be truncated in the PDF manual.
tfDetails: no visible global function definition for ‘start’
tfDetails: no visible global function definition for ‘end’
Undefined global functions or variables:
  end start
Consider adding
  importFrom("stats", "end", "start")
to your NAMESPACE file.
Qhat: no visible global function definition for ‘pnorm’
plrt: no visible global function definition for ‘uniroot’
plrt: no visible global function definition for ‘optimize’
simulatedata: no visible global function definition for ‘rnorm’
tsc.test: no visible global function definition for ‘shapiro.test’
tsc.test: no visible global function definition for ‘p.adjust’
tsc.test: no visible global function definition for ‘glm’
tsc.test : f: no visible global function definition for ‘pnorm’
tsc.test: no visible global function definition for ‘uniroot’
tsc.test: no visible global function definition for ‘optimize’
variance: no visible global function definition for ‘density’
variance: no visible global function definition for ‘ecdf’
Undefined global functions or variables:
  density ecdf glm optimize p.adjust pnorm rnorm shapiro.test uniroot
Consider adding
  importFrom("stats", "density", "ecdf", "glm", "optimize", "p.adjust",
             "pnorm", "rnorm", "shapiro.test", "uniroot")
to your NAMESPACE file.
File ‘tsc/libs/tsc.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘tsDyn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: selectHyperParms
> ### Title: Automatic selection of model hyper-parameters
> ### Aliases: selectLSTAR selectNNET
> ### Keywords: ts
> 
> ### ** Examples
> 
> llynx <- log10(lynx)
> selectLSTAR(llynx, m=2)
Error in if (!is.na(start.con$candidates)) { : 
  the condition has length > 1
Calls: selectLSTAR -> lstar
Execution halted
Package in Depends field not imported from: ‘deSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following apparent S3 methods exported but not registered:
  plot.ami plot.d2 plot.false.nearest print.d2 print.false.nearest
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'sim.cont.Rd':
  \examples lines wider than 100 characters:
     rossler.ts <- sim.cont(rossler.syst, start=0, end=650, dt=0.1, start.x=c(0,0,0), parms=c(0.15, 0.2, 10))

These lines will be truncated in the PDF manual.
File ‘tseriesChaos/libs/tseriesChaos.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vintageMap: no visible global function definition for ‘read.table’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameLocalConnection: no visible global function
  definition for ‘frequency’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘as.ts’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘zoo’
TSget,character-TSfameServerConnection: no visible global function
  definition for ‘frequency’
Undefined global functions or variables:
  as.ts frequency read.table zoo
Consider adding
  importFrom("stats", "as.ts", "frequency")
  importFrom("utils", "read.table")
to your NAMESPACE file.
DstandardizedLoadings.TSFmodel: no visible global function definition
  for ‘cov’
FAfitStats.TSFmodel: no visible global function definition for ‘cov’
FAfitStats.default: no visible global function definition for ‘cor’
FAfitStats.default: no visible global function definition for
  ‘factanal’
FAfitStats.default: no visible global function definition for ‘pchisq’
FAmodelFitStats: no visible global function definition for ‘pchisq’
checkResiduals.TSFmodel: no visible global function definition for
  ‘cov’
distribution.factorsEstEval: no visible global function definition for
  ‘par’
distribution.factorsEstEval: no visible binding for global variable
  ‘par’
distribution.factorsEstEval: no visible global function definition for
  ‘density’
distribution.factorsEstEval: no visible global function definition for
  ‘matplot’
distribution.factorsEstEval: no visible global function definition for
  ‘title’
summary.TSFmodel: no visible global function definition for ‘start’
summary.TSFmodel: no visible global function definition for ‘end’
Undefined global functions or variables:
  cor cov density end factanal matplot par pchisq start title
Consider adding
  importFrom("graphics", "matplot", "par", "title")
  importFrom("stats", "cor", "cov", "density", "end", "factanal",
             "pchisq", "start")
to your NAMESPACE file.
Func.SAX: no visible global function definition for ‘sd’
Func.SAX: no visible global function definition for ‘qnorm’
Func.matrix: no visible global function definition for ‘qnorm’
Func.motif: no visible global function definition for ‘sd’
Func.motif: no visible global function definition for ‘na.omit’
Func.motif: no visible global function definition for ‘combn’
Func.motif.multivariate: no visible global function definition for
  ‘txtProgressBar’
Func.motif.multivariate: no visible global function definition for
  ‘setTxtProgressBar’
Undefined global functions or variables:
  combn na.omit qnorm sd setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "na.omit", "qnorm", "sd")
  importFrom("utils", "combn", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
dLag : dlag.f: no visible global function definition for
  ‘complete.cases’
distmat: no visible global function definition for ‘dist’
fitCity: no visible global function definition for ‘glm.control’
fitCity: no visible global function definition for ‘terms’
ldmvnorm: no visible global function definition for ‘mahalanobis’
lspline: no visible global function definition for ‘quantile’
plot.tsdecomp: no visible global function definition for ‘par’
plot.tsdecomp: no visible global function definition for ‘plot’
setupFormula: no visible global function definition for ‘as.formula’
spatialgibbs: no visible global function definition for ‘rnorm’
spatialgibbs: no visible global function definition for ‘rgamma’
spatialgibbs: no visible global function definition for ‘runif’
tsdecomp: no visible global function definition for ‘fft’
Undefined global functions or variables:
  as.formula complete.cases dist fft glm.control mahalanobis par plot
  quantile rgamma rnorm runif terms
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "complete.cases", "dist", "fft",
             "glm.control", "mahalanobis", "quantile", "rgamma", "rnorm",
             "runif", "terms")
to your NAMESPACE file.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of ‘penalize.diag’ to
  ‘penalize.diagonal’
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
File ‘tspmeta/libs/tspmeta.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TT.GS : TT.GS.sp: no visible global function definition for ‘qt’
TT.GS : TT.GS.sp: no visible global function definition for ‘runif’
TT.GS : TT.GS.sp: no visible global function definition for ‘pt’
TT.moment: no visible global function definition for ‘dt’
TT.moment: no visible global function definition for ‘pt’
Undefined global functions or variables:
  dt pt qt runif
Consider adding
  importFrom("stats", "dt", "pt", "qt", "runif")
to your NAMESPACE file.
ttScreening: no visible global function definition for ‘gaussian’
ttScreening: no visible global function definition for ‘glm.control’
ttScreening: no visible global function definition for ‘model.response’
ttScreening: no visible global function definition for ‘is.empty.model’
ttScreening: no visible global function definition for ‘model.matrix’
ttScreening: no visible global function definition for ‘na.omit’
ttScreening: no visible global function definition for ‘terms’
ttScreening: no visible global function definition for ‘capture.output’
ttScreening: no visible global function definition for ‘glm’
ttScreening: no visible binding for global variable ‘gaussian’
ttScreening: no visible global function definition for ‘pt’
ttScreening: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  capture.output gaussian glm glm.control is.empty.model model.matrix
  model.response na.omit p.adjust pt terms
Consider adding
  importFrom("stats", "gaussian", "glm", "glm.control", "is.empty.model",
             "model.matrix", "model.response", "na.omit", "p.adjust",
             "pt", "terms")
  importFrom("utils", "capture.output")
to your NAMESPACE file.
.saveDevice: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  dev.off
Consider adding
  importFrom("grDevices", "dev.off")
to your NAMESPACE file.
ttwa: no visible global function definition for ‘aggregate’
ttwa: no visible global function definition for ‘txtProgressBar’
ttwa: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  aggregate setTxtProgressBar txtProgressBar
Consider adding
  importFrom("stats", "aggregate")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
Running examples in ‘tuckerR.mmgg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot
> ### Title: Plot an interactive Biplot
> ### Aliases: plot plot.marta
> 
> ### ** Examples
> 
> data(maize_pop,package = "tuckerR.mmgg")
> prueba1 <- tucker2R(maize_pop, amb=2, stand=TRUE, nc1=3, nc2=3)
> plot(prueba1)
Error in UseMethod("plot") : 
  no applicable method for 'plot' applied to an object of class "c('double', 'numeric')"
Calls: plot -> plot.marta -> plot
Execution halted
http.connection: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘gsl’ ‘igraph’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following apparent S3 methods exported but not registered:
  predict.TuneParetoModel print.TuneParetoClassifier
  print.TuneParetoModel print.TuneParetoResult
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘TunePareto/libs/TunePareto.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
turf: no visible global function definition for ‘read.table’
turf: no visible global function definition for ‘flush.console’
turf.combos: no visible global function definition for ‘combn’
Undefined global functions or variables:
  combn flush.console read.table
Consider adding
  importFrom("utils", "combn", "flush.console", "read.table")
to your NAMESPACE file.
File ‘TUWmodel/libs/TUWmodel.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tvd/libs/tvd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘tweenr/libs/tweenr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
TwoCop: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘TwoCop/libs/TwoCop.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘TwoPhaseInd/libs/TwoPhaseInd.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  print.twoStageGwasPower print.twoStageNull
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
condnorm: no visible global function definition for ‘pnorm’
condnorm: no visible global function definition for ‘dnorm’
find.p.joint: no visible global function definition for ‘integrate’
find.p.joint.alt: no visible global function definition for ‘integrate’
termsInt: no visible global function definition for ‘pnorm’
termsInt.alt: no visible global function definition for ‘pnorm’
twoStageNull: no visible global function definition for ‘qnorm’
twoStageNull: no visible global function definition for ‘optimize’
twoStagePower: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm integrate optimize pnorm qnorm
Consider adding
  importFrom("stats", "dnorm", "integrate", "optimize", "pnorm", "qnorm")
to your NAMESPACE file.
Rd file 'twoStageGwasPower.Rd':
  \usage lines wider than 90 characters:
     twoStageGwasPower(pD, pG, grr, inheritance = "multiplicative", pi.samples, pi.markers, alpha.marker, n.cases, n.controls)

These lines will be truncated in the PDF manual.
txtacf: no visible binding for global variable ‘na.fail’
txtacf: no visible global function definition for ‘acf’
txtboxplot : <anonymous>: no visible global function definition for
  ‘boxplot.stats’
txtboxplot: no visible global function definition for ‘boxplot.stats’
txtdensity: no visible global function definition for ‘density’
Undefined global functions or variables:
  acf boxplot.stats density na.fail
Consider adding
  importFrom("grDevices", "boxplot.stats")
  importFrom("stats", "acf", "density", "na.fail")
to your NAMESPACE file.
Crm: no visible global function definition for ‘integrate’
Crm : <anonymous>: no visible global function definition for
  ‘integrate’
Crm: no visible global function definition for ‘optimize’
ail1: no visible global function definition for ‘uniroot’
ail2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ail2: no visible global function definition for ‘uniroot’
aip : fu : <anonymous>: no visible global function definition for
  ‘integrate’
aip: no visible global function definition for ‘uniroot’
ait1: no visible global function definition for ‘uniroot’
ait2 : fu : <anonymous>: no visible global function definition for
  ‘integrate’
ait2: no visible global function definition for ‘uniroot’
sim3p3: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘rbinom’
simCrm: no visible global function definition for ‘palette’
simCrm: no visible global function definition for ‘gray’
simCrm: no visible global function definition for ‘plot’
simCrm: no visible global function definition for ‘abline’
simCrm: no visible global function definition for ‘lines’
ssim3p3: no visible global function definition for ‘txtProgressBar’
ssim3p3: no visible global function definition for ‘setTxtProgressBar’
ssimCrm: no visible global function definition for ‘txtProgressBar’
ssimCrm: no visible global function definition for ‘setTxtProgressBar’
Undefined global functions or variables:
  abline gray integrate lines optimize palette plot rbinom
  setTxtProgressBar txtProgressBar uniroot
Consider adding
  importFrom("grDevices", "gray", "palette")
  importFrom("graphics", "abline", "lines", "plot")
  importFrom("stats", "integrate", "optimize", "rbinom", "uniroot")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
rmd2pdf: no visible global function definition for ‘tail’
rnw2pdf: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
File ‘ucminf/libs/ucminf.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘udunits2/libs/udunits2.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'dataItemExplorer.Rd':
  \usage lines wider than 90 characters:
       apiurl = "http://marketinformation.natgrid.co.uk/MIPIws-public/public/publicwebservice.asmx")

These lines will be truncated in the PDF manual.
ubRacing : predCandidate: no visible global function definition for
  ‘predict’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘pchisq’
ubRacing : aux2.friedman.edit: no visible global function definition
  for ‘qt’
ubRacing : aux.friedman.edit: no visible global function definition for
  ‘wilcox.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘t.test’
ubRacing : aux.ttest.edit: no visible global function definition for
  ‘p.adjust’
ubRacing : idFolds: no visible global function definition for
  ‘quantile’
ubRacing: no visible binding for global variable ‘sd’
ubSmoteExs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  p.adjust pchisq predict qt quantile runif sd t.test wilcox.test
Consider adding
  importFrom("stats", "p.adjust", "pchisq", "predict", "qt", "quantile",
             "runif", "sd", "t.test", "wilcox.test")
to your NAMESPACE file.
med: no visible global function definition for ‘quantile’
uh: no visible global function definition for ‘mad’
uh.bu: no visible global function definition for ‘mad’
Undefined global functions or variables:
  mad quantile
Consider adding
  importFrom("stats", "mad", "quantile")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  predict.uniCox print.uniCoxCVFit print.uniCoxFit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
permute.rows: no visible global function definition for ‘runif’
uniCox: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘quantile’
uniCoxCV: no visible global function definition for ‘coxph’
uniCoxCV: no visible binding for global variable ‘var’
Undefined global functions or variables:
  coxph quantile runif var
Consider adding
  importFrom("stats", "quantile", "runif", "var")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'predict.uniCox':
  ‘predict.uniCox’

S3 methods shown with full name in documentation object 'uniCox-internal':
  ‘print.uniCoxCVFit’ ‘print.uniCoxFit’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
File ‘uniCox/libs/uniCox.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dudewicz.unif.test: no visible global function definition for ‘runif’
frosini.unif.test: no visible global function definition for ‘runif’
hegazy.unif.test: no visible global function definition for ‘runif’
kolmogorov.unif.test: no visible global function definition for ‘runif’
kuiper.unif.test: no visible global function definition for ‘runif’
neyman.unif.test: no visible global function definition for ‘runif’
quesenberry.unif.test: no visible global function definition for
  ‘runif’
sarkadi.unif.test: no visible global function definition for ‘runif’
sherman.unif.test: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
cumcount: no visible global function definition for ‘setNames’
uniqtag: no visible global function definition for ‘setNames’
Undefined global functions or variables:
  setNames
Consider adding
  importFrom("stats", "setNames")
to your NAMESPACE file.
File ‘unsystation/libs/unsystation.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.upclassfit print.upclassfit summary.upclassfit
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
plot.upclassfit: no visible global function definition for ‘frame’
plot.upclassfit: no visible global function definition for ‘par’
plot.upclassfit: no visible global function definition for ‘axis’
plot.upclassfit: no visible global function definition for ‘matplot’
plot.upclassfit: no visible global function definition for ‘legend’
plot.upclassfit: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
Running examples in ‘upclass-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.upclassfit
> ### Title: Plot for upclassfit
> ### Aliases: plot.upclassfit plot
> ### Keywords: Classification
> 
> ### ** Examples
> 
> data(wine, package = "gclus")
> X <- as.matrix(wine[, -1])
> cl <- unclass(wine[, 1])
> indtrain <- sort(sample(1:178, 120))
> indtest <- setdiff(1:178, indtrain)
> 
> fitup <- upclassify(X[indtrain,], cl[indtrain], X[indtest,], cl[indtest])
> plot(fitup)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
File ‘urca/libs/urca.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘uroot/libs/uroot.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘USAboundariesData’
readSEER: no visible global function definition for ‘read.fwf’
Undefined global functions or variables:
  read.fwf
Consider adding
  importFrom("utils", "read.fwf")
to your NAMESPACE file.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000cdp/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000cdp\").\n")
    cat("Type help(package=\"UScensus2000cdp\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File ‘UScensus2000tract/R/zzz.R’:
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat(paste("copyright (c) 2009, Zack W. Almquist, University of California-Irvine\n",     sep = ""))
    cat("For citation information, type citation(\"UScensus2000tract\").\n")
    cat("Type help(package=\"UScensus2000tract\") to get started.\n")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.
Found the following hidden files and directories:
  data/.Rhistory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'MSA.Rd':
  \usage lines wider than 90 characters:
     MSA(msafips = NULL, msaname = NULL, state=NULL , statefips=FALSE, level = c("tract", "blk", "blkgrp"), proj = NULL)

Rd file 'areaPoly.Rd':
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"den00",color = list(fun = "rainbow", attr = list(4)),main="2010 US Counties \n Oregon",type="plot",border=" ... [TRUNCATED]

Rd file 'choropleth.Rd':
  \usage lines wider than 90 characters:
     choropleth(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0.6, 0 ... [TRUNCATED]
  \examples lines wider than 100 characters:
     choropleth(oregon.county10,"P0010001",color = list(fun = "rainbow", attr = list(4)),main="2010 Counties \n Oregon",type="plot",border=" ... [TRUNCATED]
     choropleth(oregon.county10,"P0010001",main="2010 Counties \n Oregon",border="transparent",type="spplot")

Rd file 'choropleth.plot.Rd':
  \usage lines wider than 90 characters:
     choropleth.plot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, 0 ... [TRUNCATED]

Rd file 'choropleth.spplot.Rd':
  \usage lines wider than 90 characters:
     choropleth.spplot(sp, dem = "P0010001", cuts = list("quantile", seq(0, 1, 0.25)), color = list(fun = "hsv", attr = list(h = c(0.4, 0.5, ... [TRUNCATED]

Rd file 'county.Rd':
  \usage lines wider than 90 characters:
     county(fips = NULL, name = NULL, state, level = c("tract", "blk", "blkgrp"), statefips = FALSE, sp.object=NULL, proj=NULL)

These lines will be truncated in the PDF manual.
Running examples in ‘useful-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.kmeans
> ### Title: plot.kmeans
> ### Aliases: plot.kmeans
> 
> ### ** Examples
> 
> 
> k1 <- kmeans(x=iris[, 1:4], centers=3)
> plot(k1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
File ‘utf8latex/libs/utf8latex.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’
File ‘uuid/libs/uuid.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
histw: no visible global function definition for ‘plot.new’
histw: no visible global function definition for ‘plot.window’
histw: no visible global function definition for ‘axis’
histw: no visible global function definition for ‘rect’
histw: no visible global function definition for ‘lines’
uwham.boot: no visible binding for global variable ‘var’
Undefined global functions or variables:
  axis lines plot.new plot.window rect var
Consider adding
  importFrom("graphics", "axis", "lines", "plot.new", "plot.window",
             "rect")
  importFrom("stats", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Quitting from lines 92-93 (regress_intro.Rmd) 
Error: processing vignette ‘regress_intro.Rmd’ failed with diagnostics:
object ‘ttodth’ not found
Execution halted
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
File ‘validatejsonr/libs/validatejsonr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘valorate/libs/valorate.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘varband/libs/varband.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Mammen: no visible global function definition for ‘runif’
PR2: no visible global function definition for ‘ar.burg’
PR2: no visible global function definition for ‘pt’
PR2: no visible global function definition for ‘pf’
PR3: no visible global function definition for ‘ar.burg’
PR3: no visible global function definition for ‘pt’
PR3: no visible global function definition for ‘pf’
VAR.FOR: no visible global function definition for ‘qnorm’
VAR.ForeB: no visible global function definition for ‘runif’
VAR.LRtest: no visible global function definition for ‘pchisq’
VAR.LRtest: no visible global function definition for ‘pf’
VAR.PI: no visible global function definition for ‘quantile’
VAR.Waldtest: no visible global function definition for ‘pf’
VAR.irf: no visible global function definition for ‘par’
VAR.irf: no visible global function definition for ‘plot’
VAR.irf: no visible global function definition for ‘abline’
VAR1.sim: no visible global function definition for ‘rnorm’
resamp: no visible global function definition for ‘runif’
Undefined global functions or variables:
  abline ar.burg par pchisq pf plot pt qnorm quantile rnorm runif
Consider adding
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "ar.burg", "pchisq", "pf", "pt", "qnorm",
             "quantile", "rnorm", "runif")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘Todo’
Packages in Depends field not imported from:
  ‘MASS’ ‘strucchange’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
black_scholes: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  pnorm
Consider adding
  importFrom("stats", "pnorm")
to your NAMESPACE file.
burdenPlot: no visible global function definition for ‘density’
burdenPlot: no visible global function definition for ‘axis’
burdenPlot: no visible global function definition for ‘points’
burdenPlot: no visible global function definition for ‘lines’
burdenPlot: no visible global function definition for ‘abline’
burdenPlot: no visible global function definition for ‘text’
burdenPlot: no visible global function definition for ‘sd’
burdenPlot: no visible global function definition for ‘segments’
vbdm: no visible global function definition for ‘var’
vbdm: no visible global function definition for ‘pchisq’
vbdmR : run_discrete_mixture_vanilla: no visible global function
  definition for ‘var’
vbdmR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  abline axis density lines pchisq points sd segments text var
Consider adding
  importFrom("graphics", "abline", "axis", "lines", "points", "segments",
             "text")
  importFrom("stats", "density", "pchisq", "sd", "var")
to your NAMESPACE file.
File ‘vbdm/libs/vbdm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘VBLPCM/libs/VBLPCM.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
compute_KL : rtnorm: no visible global function definition for ‘runif’
compute_KL : rtnorm: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘qnorm’
compute_KL: no visible global function definition for ‘dnorm’
compute_KL: no visible global function definition for ‘pnorm’
compute_KL: no visible global function definition for ‘var’
compute_KL: no visible global function definition for ‘rbinom’
compute_KL: no visible global function definition for ‘rnorm’
compute_KL: no visible global function definition for ‘sd’
vbsr: no visible global function definition for ‘qchisq’
vbsr: no visible global function definition for ‘var’
vbsr: no visible global function definition for ‘pchisq’
vbsr: no visible global function definition for ‘sd’
vbsr: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  dnorm pchisq pnorm qchisq qnorm rbinom rnorm runif sd var
Consider adding
  importFrom("stats", "dnorm", "pchisq", "pnorm", "qchisq", "qnorm",
             "rbinom", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
File ‘vbsr/libs/vbsr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
cv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
File ‘VDA/libs/VDA.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Compare2FDS: no visible global function definition for ‘runif’
Compare2FDS: no visible global function definition for ‘lm’
Compare2FDS: no visible global function definition for ‘model.matrix’
Compare2FDS: no visible global function definition for ‘plot’
Compare2FDS: no visible global function definition for ‘abline’
Compare2FDS: no visible global function definition for ‘lines’
Compare2FDS: no visible global function definition for ‘text’
Compare2Vdg: no visible global function definition for ‘par’
Compare2Vdg: no visible global function definition for ‘plot’
Compare2Vdg: no visible global function definition for ‘lines’
Compare2Vdg: no visible global function definition for ‘legend’
FDSPlot: no visible global function definition for ‘runif’
FDSPlot: no visible global function definition for ‘lm’
FDSPlot: no visible global function definition for ‘model.matrix’
FDSPlot: no visible global function definition for ‘plot’
FDSPlot: no visible global function definition for ‘abline’
Vdgraph: no visible global function definition for ‘par’
Vdgraph: no visible global function definition for ‘plot’
Vdgraph: no visible global function definition for ‘lines’
Vdgraph: no visible global function definition for ‘legend’
Undefined global functions or variables:
  abline legend lines lm model.matrix par plot runif text
Consider adding
  importFrom("graphics", "abline", "legend", "lines", "par", "plot",
             "text")
  importFrom("stats", "lm", "model.matrix", "runif")
to your NAMESPACE file.
File ‘Vdgraph/libs/Vdgraph.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vdg/libs/vdg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
calculateParameters,AffineTransformation: no visible global function
  definition for ‘lm’
calculateParameters,AffineTransformation: no visible global function
  definition for ‘coef’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘lm’
calculateParameters,SimilarityTransformation: no visible global
  function definition for ‘coef’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘points’
plotGridTransformation,Cartesian2DCoordinateTransformation: no visible
  global function definition for ‘legend’
Undefined global functions or variables:
  coef legend lm points
Consider adding
  importFrom("graphics", "legend", "points")
  importFrom("stats", "coef", "lm")
to your NAMESPACE file.
DrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
'library' or 'require' call to ‘stats’ which was already attached by Depends.
  Please remove these calls from your code.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of ‘arg’ to ‘args’
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of ‘arg’ to
  ‘args’
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of ‘arg’ to ‘args’
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of ‘arg’ to ‘args’
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of ‘arg’ to ‘args’
prepare_Rd: H.Rd:41-42: Dropping empty section \note
prepare_Rd: M.homog.Rd:19-21: Dropping empty section \details
prepare_Rd: M.homog.Rd:35-36: Dropping empty section \note
prepare_Rd: Rel.homog.Rd:24-25: Dropping empty section \note
prepare_Rd: bootstrap.Rd:34: Dropping empty section \note
prepare_Rd: d.Rd:35-36: Dropping empty section \note
prepare_Rd: normalize.rows.Rd:26-27: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:23-24: Dropping empty section \note
prepare_Rd: p.q.sum.Rd:26: Dropping empty section \examples
prepare_Rd: sim.groups.Rd:27-28: Dropping empty section \note
prepare_Rd: sim.table.Rd:25-26: Dropping empty section \note
prepare_Rd: similarity.Rd:25-26: Dropping empty section \note
prepare_Rd: turnover.Rd:17-18: Dropping empty section \details
prepare_Rd: turnover.Rd:29-30: Dropping empty section \note
plot.VennDiagram : <anonymous>: no visible global function definition
  for ‘hcl’
plot.VennDiagram: no visible global function definition for ‘plot.new’
plot.VennDiagram: no visible global function definition for
  ‘plot.window’
plot.VennDiagram: no visible global function definition for ‘col2rgb’
plot.VennDiagram: no visible global function definition for ‘rgb’
plot.VennDiagram: no visible global function definition for ‘polygon’
plot.VennDiagram: no visible global function definition for ‘text’
plot.VennDiagram: no visible global function definition for ‘title’
Undefined global functions or variables:
  col2rgb hcl plot.new plot.window polygon rgb text title
Consider adding
  importFrom("grDevices", "col2rgb", "hcl", "rgb")
  importFrom("graphics", "plot.new", "plot.window", "polygon", "text",
             "title")
to your NAMESPACE file.
File ‘vertexenum/libs/vertexenum.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls not declared from:
  ‘ggplot2’ ‘magrittr’
File ‘VIFCP/libs/VIFCP.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
vif: no visible global function definition for ‘sd’
vif: no visible global function definition for ‘lm’
vif: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  lm pnorm sd
Consider adding
  importFrom("stats", "lm", "pnorm", "sd")
to your NAMESPACE file.
Rd file 'vif.Rd':
  \usage lines wider than 90 characters:
             vif(y, x, w0 = 0.05, dw = 0.05, subsize = 200, trace = TRUE, mode = c("dense", "sparse"))
  \examples lines wider than 100 characters:
             vif.sel <- vif(housingexp$y, housingexp$x, w0 = 0.0005, dw = 0.005, subsize = 300, trace = FALSE);

These lines will be truncated in the PDF manual.
hyperpara: no visible binding for global variable ‘var’
hyperpara: no visible global function definition for ‘hist’
Undefined global functions or variables:
  hist var
Consider adding
  importFrom("graphics", "hist")
  importFrom("stats", "var")
to your NAMESPACE file.
File ‘VIGoR/libs/VIGoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘vines/libs/vines.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
panel.meansdplot : meansdplot.stats: no visible global function
  definition for ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
prepare_Rd: panel.meansdplot.Rd:42-45: Dropping empty section \value
prepare_Rd: panel.meansdplot.Rd:49-51: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:40-42: Dropping empty section \details
prepare_Rd: panel.violinm.Rd:43-49: Dropping empty section \value
prepare_Rd: panel.violinm.Rd:53-55: Dropping empty section \note
prepare_Rd: panel.violinm.Rd:50-52: Dropping empty section \author
prepare_Rd: violinmplot.Rd:34-36: Dropping empty section \details
prepare_Rd: violinmplot.Rd:48-50: Dropping empty section \note
Package in Depends field not imported from: ‘sm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
vioplot: no visible global function definition for ‘quantile’
vioplot: no visible global function definition for ‘median’
vioplot: no visible global function definition for ‘plot.new’
vioplot: no visible global function definition for ‘plot.window’
vioplot: no visible global function definition for ‘axis’
vioplot: no visible global function definition for ‘box’
vioplot: no visible global function definition for ‘polygon’
vioplot: no visible global function definition for ‘lines’
vioplot: no visible global function definition for ‘rect’
vioplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  axis box lines median plot.new plot.window points polygon quantile
  rect
Consider adding
  importFrom("graphics", "axis", "box", "lines", "plot.new",
             "plot.window", "points", "polygon", "rect")
  importFrom("stats", "median", "quantile")
to your NAMESPACE file.
viopoints.default: no visible global function definition for ‘par’
viopoints.default: no visible global function definition for ‘plot.new’
viopoints.default: no visible global function definition for
  ‘plot.window’
viopoints.default: no visible global function definition for ‘axis’
viopoints.default: no visible global function definition for ‘arrows’
viopoints.default: no visible global function definition for
  ‘getFromNamespace’
viopoints.default: no visible global function definition for ‘title’
viopoints.default: no visible global function definition for ‘box’
Undefined global functions or variables:
  arrows axis box getFromNamespace par plot.new plot.window title
Consider adding
  importFrom("graphics", "arrows", "axis", "box", "par", "plot.new",
             "plot.window", "title")
  importFrom("utils", "getFromNamespace")
to your NAMESPACE file.
'::' or ':::' import not declared from: ‘gdtools’
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
ViSiElse 6.516  0.027   9.349
File ‘vita/libs/vita.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Decile.Plot: no visible global function definition for ‘barplot’
Decile.Plot: no visible global function definition for ‘axis’
Sliding.Window: no visible global function definition for ‘plot’
Sliding.Window: no visible global function definition for ‘lines’
Sliding.Window: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis barplot legend lines plot
Consider adding
  importFrom("graphics", "axis", "barplot", "legend", "lines", "plot")
to your NAMESPACE file.
RCplot: no visible global function definition for ‘residuals’
RCplot: no visible global function definition for ‘predict’
RCplot: no visible global function definition for ‘par’
RCplot: no visible global function definition for ‘plot.new’
RCplot: no visible global function definition for ‘plot.window’
RCplot: no visible global function definition for ‘strwidth’
RCplot: no visible global function definition for ‘plot’
RCplot: no visible global function definition for ‘abline’
RCplot: no visible global function definition for ‘text’
RCplot: no visible global function definition for ‘mtext’
fitted.vlmc: no visible global function definition for ‘predict’
print.vlmc: no visible global function definition for ‘AIC’
residuals.vlmc: no visible global function definition for ‘predict’
simulate.vlmc: no visible global function definition for ‘runif’
summary.vlmc: no visible global function definition for ‘predict’
vlmc: no visible global function definition for ‘qchisq’
Undefined global functions or variables:
  AIC abline mtext par plot plot.new plot.window predict qchisq
  residuals runif strwidth text
Consider adding
  importFrom("graphics", "abline", "mtext", "par", "plot", "plot.new",
             "plot.window", "strwidth", "text")
  importFrom("stats", "AIC", "predict", "qchisq", "residuals", "runif")
to your NAMESPACE file.
File ‘VLMC/libs/VLMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
voss1d: no visible global function definition for ‘approx’
voss1d: no visible global function definition for ‘rnorm’
voss1g: no visible global function definition for ‘dchisq’
voss1g: no visible global function definition for ‘approx’
voss1g: no visible global function definition for ‘rnorm’
voss2d: no visible global function definition for ‘rnorm’
voss2g: no visible global function definition for ‘dchisq’
voss2g: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  approx dchisq rnorm
Consider adding
  importFrom("stats", "approx", "dchisq", "rnorm")
to your NAMESPACE file.
'library' or 'require' call to ‘raster’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
level: no visible global function definition for ‘quantile’
obj.rec: no visible global function definition for ‘txtProgressBar’
obj.rec: no visible global function definition for ‘setTxtProgressBar’
project: no visible global function definition for ‘aggregate’
raster.proj: no visible global function definition for ‘quantile’
raster.proj: no visible global function definition for ‘rasterFromXYZ’
raster.proj: no visible global function definition for ‘plot.new’
raster.proj: no visible global function definition for ‘plot’
raster.proj: no visible global function definition for ‘legend’
sub.obj: no visible global function definition for ‘aggregate’
sub.obj: no visible global function definition for ‘txtProgressBar’
sub.obj: no visible global function definition for ‘setTxtProgressBar’
surface: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  aggregate legend plot plot.new quantile rasterFromXYZ
  setTxtProgressBar txtProgressBar
Consider adding
  importFrom("graphics", "legend", "plot", "plot.new")
  importFrom("stats", "aggregate", "quantile")
  importFrom("utils", "setTxtProgressBar", "txtProgressBar")
to your NAMESPACE file.
'library' or 'require' call to ‘misc3d’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
plot.vscc: no visible global function definition for ‘rainbow’
plot.vscc: no visible global function definition for ‘pairs’
Undefined global functions or variables:
  pairs rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "pairs")
to your NAMESPACE file.
Non-standard file/directory found at top level:
  ‘vwr-Ex.R’
Packages in Depends field not imported from:
  ‘lattice’ ‘latticeExtra’ ‘stringdist’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ald: no visible global function definition for ‘detectCores’
ald: no visible global function definition for ‘mclapply’
coltheart.N: no visible global function definition for ‘detectCores’
coltheart.N: no visible global function definition for ‘mclapply’
hamming.distance: no visible global function definition for
  ‘stringdist’
ldknn: no visible global function definition for ‘detectCores’
ldknn: no visible global function definition for ‘mclapply’
ldknn.odds: no visible global function definition for ‘glm’
ldknn.odds: no visible binding for global variable ‘binomial’
ldknn.odds: no visible global function definition for ‘coefficients’
levenshtein.damerau.distance: no visible global function definition for
  ‘stringdist’
levenshtein.distance: no visible global function definition for
  ‘stringdist’
plot.ldknn.run: no visible global function definition for ‘histogram’
plot.ldknn.run: no visible global function definition for
  ‘theEconomist.theme’
plot.ldknn.run: no visible global function definition for ‘xyplot’
plot.ldknn.run: no visible global function definition for ‘as.layer’
Undefined global functions or variables:
  as.layer binomial coefficients detectCores glm histogram mclapply
  stringdist theEconomist.theme xyplot
Consider adding
  importFrom("stats", "binomial", "coefficients", "glm")
to your NAMESPACE file.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rd file 'waffect-package.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 5 individuals, 2 cases, 3 controls, the probab ... [TRUNCATED]
     ## Not run: Simulation of phenotypes in the multiclass case (in this example: 4 individuals and  3 classes, 1 individual in class 1, 2  ... [TRUNCATED]

Rd file 'waffect.Rd':
  \examples lines wider than 100 characters:
     ## Not run: Typical usage to simulate case/control phenotypes under H1 (in this example: 12 individuals, 7 cases, 5 controls, the proba ... [TRUNCATED]
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=c(7,5), label=c(1,0))
     waffect(prob =  c(0.2, 0.4, 0.9, 0.6, 0.9, 0.1, 0.4, 0.6, 0.6, 0.3, 0.8, 0.1), count=7, label=c(1,0))
     ## Not run: If prob is not specified then a constant vector of probabilities is assumed by default. This is equivalent to simulate phen ... [TRUNCATED]

These lines will be truncated in the PDF manual.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’
File ‘waffect/libs/waffect.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
summary.whc: no visible global function definition for ‘printCoefmat’
wahc.fit: no visible global function definition for ‘pt’
wahc.fit: no visible global function definition for ‘cor’
whc: no visible global function definition for ‘model.frame’
whc: no visible global function definition for ‘model.matrix’
whc: no visible global function definition for ‘model.response’
Undefined global functions or variables:
  cor model.frame model.matrix model.response printCoefmat pt
Consider adding
  importFrom("stats", "cor", "model.frame", "model.matrix",
             "model.response", "printCoefmat", "pt")
to your NAMESPACE file.
'::' or ':::' import not declared from: ‘XML’
'library' or 'require' call not declared from: ‘XML’
File ‘wand/libs/wand.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Rd file 'p.storage.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

Rd file 'read.results.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]

Rd file 'wasim-package.Rd':
  \examples lines wider than 100 characters:
     d.wasim.out <- read.results("", "weisseritz",ts.length=21937,subcatchments=2, ending="ww100.txt")    # Datensatz heisst jetzt d.wasim.o ... [TRUNCATED]
     d.meas.all<-read.table("weisseritz/ww100-rh.txt",header=TRUE, na.strings ="999", skip=4)  # gemessene Daten einlesen

These lines will be truncated in the PDF manual.
Foreign function call to a different package:
  .C("comwr", ..., PACKAGE = "wavethresh")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.wvd summary.wvd
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Rd file 'FWaveD.Rd':
  \usage lines wider than 90 characters:
     FWaveD(y, g = 1, L = 3, deg = 3, F = (log2(length(y)) - 1), thr = rep(0, log2(length(y))), SOFT = FALSE)

Rd file 'WaveD.Rd':
  \usage lines wider than 90 characters:
     WaveD(yobs, g = c(1, rep(0, (length(yobs) - 1))), MC = FALSE, SOFT = FALSE, F = find.j1(g, scale(yobs))[2], L = 3, deg = 3, eta = sqrt( ... [TRUNCATED]

Rd file 'multires.Rd':
  \usage lines wider than 90 characters:
     multires(wcUntrimmed, lowest = 3, coarse = 3, highestplot = NULL, descending = FALSE, sc = 1)

These lines will be truncated in the PDF manual.
Running examples in ‘waved-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.wvd
> ### Title: Plot wvd objects
> ### Aliases: plot.wvd
> ### Keywords: internal
> 
> ### ** Examples
> 
> library(waved)
> data=waved.example(TRUE,FALSE)
> doppler.wvd=WaveD(data$doppler.noisy,data$g)
> plot(doppler.wvd)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Found the following apparent S3 methods exported but not registered:
  plot.dwt plot.dwt.multiple plot.modwt print.dwt print.modwt
  print.wt.filter summary.dwt summary.modwt summary.wt.filter
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘wavelets/libs/wavelets.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  plot.dwt.2d
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘waveslim/libs/waveslim.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wavethresh/libs/wavethresh.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
changepoints.sbs: no visible global function definition for ‘mad’
changepoints.wbs: no visible global function definition for ‘var’
changepoints.wbs: no visible global function definition for ‘quantile’
plot.sbs: no visible global function definition for ‘ts.plot’
plot.sbs: no visible global function definition for ‘lines’
plot.sbs: no visible global function definition for ‘title’
random.intervals: no visible global function definition for ‘runif’
sbs.default: no visible global function definition for ‘var’
wbs.default: no visible global function definition for ‘var’
Undefined global functions or variables:
  lines mad quantile runif title ts.plot var
Consider adding
  importFrom("graphics", "lines", "title")
  importFrom("stats", "mad", "quantile", "runif", "ts.plot", "var")
to your NAMESPACE file.
File ‘wbs/libs/wbs.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following apparent S3 methods exported but not registered:
  knots.WCE
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
Running examples in ‘WCE-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: knots.WCE
> ### Title: Obtain the placement of the knots used for splines in WCE models
> ### Aliases: knots.WCE knots
> 
> ### ** Examples
> 
> 
> wce <- WCE(drugdata, "Cox", 1, 90, constrained = "R", id = "Id", event = "Event",
+ 		   start = "Start", stop = "Stop", expos = "dose", 
+ 		   covariates = c("age", "sex"))
> knots(wce)
Error in UseMethod("knots") : 
  no applicable method for 'knots' applied to an object of class "WCE"
Calls: knots
Execution halted
onesamplemeantest: no visible global function definition for ‘pnorm’
twosamplemeantest: no visible global function definition for ‘pnorm’
wcq: no visible global function definition for ‘var’
wcq: no visible global function definition for ‘pnorm’
wcq.fdrc: no visible global function definition for ‘p.adjust’
Undefined global functions or variables:
  p.adjust pnorm var
Consider adding
  importFrom("stats", "p.adjust", "pnorm", "var")
to your NAMESPACE file.
File ‘webreadr/libs/webreadr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Malformed Title field: should not end in a period.
Deprecated license: BSD
Non-standard file/directory found at top level:
  ‘webvis_0.0.1.tar.gz’
Found the following apparent S3 methods exported but not registered:
  +.webvis
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘webvis/R/zzz.R’:
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

[1] "Welcome to the webvis pacakge."
render.webvis: no visible global function definition for ‘browseURL’
unfold.webvis : <anonymous>: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  browseURL runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.webvis':
  ‘plot.webvis’

S3 methods shown with full name in documentation object '"+.webvis"':
  ‘+.webvis’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘webvis-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pv.area
> ### Title: Add a bar to the visualization.
> ### Aliases: pv.area
> ### Keywords: hplot
> 
> ### ** Examples
> # line example 1 (using layers)
> wv <- pv.panel(width=150, height=150)
> render.webvis(wv + pv.area(wv=wv, data=c(1, 1.2, 1.7, 1.5, .7, .5, .2), bottom=0, height.name="y", left.name="x", height.scale="linear.y.y", left.scale="linear.x.x"))
Error in wv + pv.area(wv = wv, data = c(1, 1.2, 1.7, 1.5, 0.7, 0.5, 0.2),  : 
  non-numeric argument to binary operator
Calls: render.webvis
Execution halted
Weighted.Box.test: no visible global function definition for ‘acf’
Weighted.Box.test: no visible binding for global variable ‘na.pass’
Weighted.Box.test: no visible global function definition for ‘pgamma’
Weighted.Box.test: no visible global function definition for ‘pchisq’
Weighted.LM.test: no visible global function definition for ‘acf’
Weighted.LM.test: no visible binding for global variable ‘na.pass’
Weighted.LM.test: no visible global function definition for ‘pgamma’
Undefined global functions or variables:
  acf na.pass pchisq pgamma
Consider adding
  importFrom("stats", "acf", "na.pass", "pchisq", "pgamma")
to your NAMESPACE file.
File ‘weightedScores/libs/weightedScores.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running ‘texi2dvi’ on ‘wgsea.tex’ failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' call to ‘markdown’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/home/hornik/tmp/R.check/r-devel-clang/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
dlog.norm: no visible global function definition for ‘rnorm’
fun.load.hals.a: no visible global function definition for ‘sfExport’
fun.load.hals.a: no visible global function definition for ‘sfLibrary’
fun.load.hals.fill: no visible global function definition for
  ‘sfExport’
fun.load.hals.fill: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.a: no visible global function definition for ‘sfExport’
fun.load.widals.a: no visible global function definition for
  ‘sfLibrary’
fun.load.widals.fill: no visible global function definition for
  ‘sfExport’
fun.load.widals.fill: no visible global function definition for
  ‘sfLibrary’
unif.mh: no visible global function definition for ‘runif’
Undefined global functions or variables:
  rnorm runif sfExport sfLibrary
Consider adding
  importFrom("stats", "rnorm", "runif")
to your NAMESPACE file.
File ‘widals/libs/widals.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
'library' or 'require' calls in package code:
  ‘genefilter’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
.onAttach: no visible global function definition for
  ‘packageDescription’
.relax.cvcompute: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.elnet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.relax.widenet.cv.lognet: no visible global function definition for
  ‘predict’
.relax.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.elnet: no visible global function definition for ‘predict’
.widenet.cv.elnet: no visible binding for global variable
  ‘weighted.mean’
.widenet.cv.lognet: no visible global function definition for ‘predict’
.widenet.cv.lognet: no visible binding for global variable
  ‘weighted.mean’
predict.widenet: no visible global function definition for ‘predict’
screen.cor : <anonymous>: no visible global function definition for
  ‘var’
screen.cor : <anonymous>: no visible global function definition for
  ‘cor.test’
screen.ttest: no visible global function definition for ‘colttests’
widenet: no visible global function definition for ‘mc.reset.stream’
widenet: no visible global function definition for ‘mclapply’
widenet: no visible global function definition for ‘predict’
Undefined global functions or variables:
  colttests cor.test mc.reset.stream mclapply packageDescription
  predict var weighted.mean
Consider adding
  importFrom("stats", "cor.test", "predict", "var", "weighted.mean")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
File ‘widenet/libs/widenet.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Bundesliga.Mannschaft: no visible global function definition for ‘data’
Bundesliga.Mannschaft: no visible binding for global variable
  ‘Bundesliga’
Bundesliga.Tabelle: no visible global function definition for ‘data’
Bundesliga.Tabelle: no visible binding for global variable ‘Bundesliga’
Bundesliga.XML: no visible global function definition for ‘data’
Bundesliga.XML: no visible binding for global variable ‘Bundesliga’
sens.spec: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  Bundesliga data na.omit
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "data")
to your NAMESPACE file.

Found the following calls to data() loading into the global environment:
File ‘wikibooks/R/Bundesliga.Mannschaft.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.Tabelle.R’:
  data(Bundesliga)
File ‘wikibooks/R/Bundesliga.XML.R’:
  data(Bundesliga)
See section ‘Good practice’ in ‘?data’.
wilcox.selection.split: no visible global function definition for
  ‘pnorm’
wilcox.test2: no visible global function definition for ‘wilcox.test’
Undefined global functions or variables:
  pnorm wilcox.test
Consider adding
  importFrom("stats", "pnorm", "wilcox.test")
to your NAMESPACE file.
Cs: no visible global function definition for ‘wilcox.test’
Don: no visible global function definition for ‘points’
Don: no visible global function definition for ‘chisq.test’
Lixn: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  chisq.test pchisq points wilcox.test
Consider adding
  importFrom("graphics", "points")
  importFrom("stats", "chisq.test", "pchisq", "wilcox.test")
to your NAMESPACE file.
plotTrait: no visible global function definition for ‘plot’
plotTrait: no visible global function definition for ‘points’
plotTrait: no visible global function definition for ‘legend’
test.windex: no visible global function definition for ‘hist’
test.windex: no visible global function definition for ‘abline’
test.windex: no visible global function definition for ‘legend’
windex: no visible global function definition for ‘sd’
windex: no visible global function definition for ‘var’
windex: no visible global function definition for ‘dist’
windex: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  abline dist hist legend plot points quantile sd var
Consider adding
  importFrom("graphics", "abline", "hist", "legend", "plot", "points")
  importFrom("stats", "dist", "quantile", "sd", "var")
to your NAMESPACE file.
File ‘wingui/libs/wingui.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wle/libs/wle.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running examples in ‘wle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anova.wle.glm.root
> ### Title: Robust Analysis of Deviance for Generalized Linear Model Fits
> ### Aliases: anova.wle.glm.root anova.wleglmlist
> ### Keywords: robust models regression
> 
> ### ** Examples
> 
> ## --- Continuing the Example from  '?wle.glm':
> ## Don't show: 
> require(utils)
> example("wle.glm", echo = FALSE)
  treatment outcome counts
1         1       1     18
2         1       2     17
3         1       3     15
4         2       1     20
5         2       2     10
6         2       3     20
7         3       1     25
8         3       2     13
9         3       3     12
Warning in predict.lm(object, newdata, se.fit, scale = 1, type = ifelse(type ==  :
  calling predict.lm(<fake-lm-object>) ...
Error in if (class(object) != "wle.glm.root") stop("Use 'extractRoot(object)' to extract a single root from a wle.glm object") : 
  the condition has length > 1
Calls: example ... withVisible -> eval -> eval -> anova -> anova.wle.glm.root
Execution halted
File ‘WMCapacity/libs/WMCapacity.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
dbayes: no visible global function definition for ‘mahalanobis’
dbayes: no visible global function definition for ‘var’
wmd: no visible global function definition for ‘cor’
wmd: no visible global function definition for ‘var’
Undefined global functions or variables:
  cor mahalanobis var
Consider adding
  importFrom("stats", "cor", "mahalanobis", "var")
to your NAMESPACE file.
fit,Leader: no visible global function definition for ‘lm’
plotfit,Leader: no visible global function definition for ‘par’
plotfit,Leader: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm par plot
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
'library' or 'require' call to ‘tm’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
File ‘wordcloud/libs/wordcloud.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘plyr’ ‘reshape2’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
wordmatch: no visible global function definition for ‘llply’
wordmatch : <anonymous>: no visible global function definition for
  ‘llply’
wordmatch: no visible global function definition for ‘melt’
wordmatch: no visible global function definition for ‘count’
Undefined global functions or variables:
  count llply melt
pickList : <anonymous>: no visible global function definition for
  ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
File ‘wordspace/libs/wordspace.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘wskm/libs/wskm.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
simul.wsvm: no visible binding for global variable ‘mixture.example’
wsvm.boost: no visible global function definition for ‘plot’
Undefined global functions or variables:
  mixture.example plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
Rd file 'simul.wsvm.Rd':
  \usage lines wider than 90 characters:
         simul.wsvm(set.seeds = 123, obs.num = 1000, mu = c(0,0), cov.mat = 0.2*diag(2), X = NULL, Y = NULL)

Rd file 'wsvm.boost.Rd':
  \usage lines wider than 90 characters:
         wsvm.boost(X, Y, new.X, new.Y, c.n, B = 50, kernel.type = list(type = "rbf", par= 0.5), C = 4, eps = 1e-10, plotting = FALSE)

These lines will be truncated in the PDF manual.
File
  inst/LICENCE
will install at top-level and is not mentioned in the DESCRIPTION file.
Non-standard file/directory found at top level:
  ‘CONTENTS’
Rd file 'classroom.Rd':
  \examples lines wider than 100 characters:
     {boxplot(classroom.first8$mathgain[classroom.first8$schoolid==i] ~ classroom.first8$classid[classroom.first8$schoolid==i],ylab="Mathgai ... [TRUNCATED]

These lines will be truncated in the PDF manual.
'::' or ':::' import not declared from: ‘lintr’
quadplot: no visible global function definition for ‘median’
xgobi: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  median write.table
Consider adding
  importFrom("stats", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
XHWE: no visible global function definition for ‘read.table’
result: no visible global function definition for ‘pchisq’
result: no visible global function definition for ‘rbinom’
result: no visible global function definition for ‘rmultinom’
Undefined global functions or variables:
  pchisq rbinom read.table rmultinom
Consider adding
  importFrom("stats", "pchisq", "rbinom", "rmultinom")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following apparent S3 methods exported but not registered:
  +.CellStyle CellBlock.default CellStyle.default
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
.xssfcolor: no visible global function definition for ‘col2rgb’
Undefined global functions or variables:
  col2rgb
Consider adding
  importFrom("grDevices", "col2rgb")
to your NAMESPACE file.
Running examples in ‘xlsx-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: CellBlock
> ### Title: Create and style a block of cells.
> ### Aliases: CellBlock CellBlock.default CB.setColData CB.setRowData
> ###   CB.setMatrixData CB.setFill CB.setFont CB.setBorder is.CellBlock
> 
> ### ** Examples
> 
> 
>   wb <- createWorkbook()
>   sheet  <- createSheet(wb, sheetName="CellBlock")
> 
>   cb <- CellBlock(sheet, 7, 3, 1000, 60)
Error in UseMethod("CellBlock") : 
  no applicable method for 'CellBlock' applied to an object of class "jobjRef"
Calls: CellBlock
Execution halted
R5.value.default: no visible binding for global variable ‘data.table’
R5.value.default: no visible global function definition for
  ‘as.data.table’
R5.value.parse: no visible binding for global variable ‘data.table’
R5.value.parse: no visible global function definition for
  ‘is.data.table’
R5.value.parse: no visible global function definition for
  ‘as.data.table’
stampme: no visible global function definition for ‘flush.console’
stampmsg: no visible global function definition for ‘flush.console’
write.data.table: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  as.data.table data.table flush.console is.data.table write.table
Consider adding
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘xml2/libs/xml2.so’:
  Found non-API calls to R: ‘R_GetConnection’, ‘R_WriteConnection’

Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard files/directories found at top level:
  ‘Bug.R’ ‘Bugs.html’ ‘Check’ ‘CodeDetails’ ‘DESCRIPTION.in’ ‘Docs’
  ‘FAQ.html’ ‘FIXME_NOW’ ‘GNUmakefile’ ‘GNUmakefile.admin’
  ‘Makevars.in’ ‘MemoryBug.R’ ‘NAMESPACE.in’ ‘NodeFuns’ ‘Notes’
  ‘QuestionSolutions’ ‘README.windows’ ‘Rsamples’ ‘TAGS’
  ‘Todo-orig.html’ ‘Todo.xml’ ‘VersionInfo’ ‘addFinalizer’ ‘checkLinks’
  ‘dotCalls’ ‘expat’ ‘index.html’ ‘index.html.in’ ‘libxml’
  ‘libxml2.9.R’ ‘scrapingData.xml’ ‘testRemoveFinalizers.R’
  ‘testRemoveFinalizers.c’ ‘xpathPointer.xml’
newXMLDoc: no visible binding for global variable ‘doc’
source: no visible binding for global variable ‘use_file’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount use_file
Rd file 'makeClassTemplate.Rd':
  \examples lines wider than 100 characters:
     "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

Rd file 'xmlClone.Rd':
  \examples lines wider than 100 characters:
     xmlParse('<doc><author id="dtl"><firstname>Duncan</firstname><surname>Temple Lang</surname></author></doc>')

Rd file 'xmlToS4.Rd':
  \examples lines wider than 100 characters:
      "<doc><part><name>ABC</name><type>XYZ</type><cost>3.54</cost><status>available</status></part></doc>"

These lines will be truncated in the PDF manual.
File ‘XML/libs/XML.so’:
  Found ‘stderr’, possibly from ‘stderr’ (C)
    Object: ‘DocParse.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
LPGM: no visible global function definition for ‘flush.console’
PGM: no visible global function definition for ‘flush.console’
PGM.path.neighborhood: no visible global function definition for
  ‘runif’
PGMSim: no visible global function definition for ‘rpois’
PGMSim: no visible global function definition for ‘par’
WPGMSim: no visible global function definition for ‘rpois’
XMRF.Sim: no visible global function definition for ‘cov2cor’
XMRF.Sim: no visible global function definition for ‘rbinom’
XMRF.Sim: no visible global function definition for ‘rnorm’
glm.generic: no visible global function definition for ‘flush.console’
mymult: no visible global function definition for ‘rmultinom’
plot.GMS: no visible global function definition for ‘pdf’
plot.GMS: no visible global function definition for ‘dev.off’
plotNet: no visible global function definition for ‘pdf’
plotNet: no visible global function definition for ‘dev.off’
print.GMS: no visible global function definition for ‘str’
processSeq: no visible binding for global variable ‘quantile’
processSeq: no visible binding for global variable ‘var’
processSeq: no visible global function definition for ‘ks.test’
rmpois : <anonymous>: no visible global function definition for ‘rpois’
Undefined global functions or variables:
  cov2cor dev.off flush.console ks.test par pdf quantile rbinom
  rmultinom rnorm rpois runif str var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "par")
  importFrom("stats", "cov2cor", "ks.test", "quantile", "rbinom",
             "rmultinom", "rnorm", "rpois", "runif", "var")
  importFrom("utils", "flush.console", "str")
to your NAMESPACE file.
File ‘XMRF/libs/XMRF.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘XNomial/libs/XNomial.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘xseq/libs/xseq.so’:
  Found no call to: ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Non-standard file/directory found at top level:
  ‘CONTRIBUTORS’
Found the following apparent S3 methods exported but not registered:
  plot.cca print.F.test.cca print.cca print.summary.cca summary.cca
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
File ‘yakmoR/libs/yakmoR.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
big.read.table: no visible global function definition for ‘read.table’
big.read.table: no visible global function definition for ‘object.size’
sparkline: no visible global function definition for ‘is.ts’
sparkline: no visible global function definition for ‘time’
sparkline: no visible global function definition for ‘boxplot’
Undefined global functions or variables:
  boxplot is.ts object.size read.table time
Consider adding
  importFrom("graphics", "boxplot")
  importFrom("stats", "is.ts", "time")
  importFrom("utils", "object.size", "read.table")
to your NAMESPACE file.
bootstrapswapcurve: no visible global function definition for ‘ts’
fitted: no visible global function definition for ‘ts’
forwardrates: no visible global function definition for ‘ts’
residuals: no visible global function definition for ‘ts’
tZC_NS: no visible global function definition for ‘cmpfun’
tZC_NS_extra: no visible global function definition for ‘cmpfun’
tZC_SV: no visible global function definition for ‘cmpfun’
tZC_SV_extra: no visible global function definition for ‘cmpfun’
ycextra: no visible global function definition for ‘new’
ycinter: no visible global function definition for ‘new’
ycplot: no visible global function definition for ‘par’
ycplot: no visible global function definition for ‘points’
ycplot: no visible global function definition for ‘abline’
ycplot: no visible global function definition for ‘hist’
ycplot: no visible global function definition for ‘lines’
ycplot: no visible global function definition for ‘density’
ycplot: no visible global function definition for ‘qqnorm’
ycplot: no visible global function definition for ‘qqline’
ycsummary: no visible global function definition for ‘shapiro.test’
ycsummary: no visible global function definition for ‘pf’
Undefined global functions or variables:
  abline cmpfun density hist lines new par pf points qqline qqnorm
  shapiro.test ts
Consider adding
  importFrom("graphics", "abline", "hist", "lines", "par", "points")
  importFrom("methods", "new")
  importFrom("stats", "density", "pf", "qqline", "qqnorm",
             "shapiro.test", "ts")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
.NS.estimator: no visible global function definition for ‘lm’
.NS.estimator: no visible global function definition for ‘coef’
.NS.estimator: no visible global function definition for ‘na.omit’
.NS.estimator: no visible global function definition for ‘resid’
.NSS.estimator: no visible global function definition for ‘lm’
.NSS.estimator: no visible global function definition for ‘coef’
.NSS.estimator: no visible global function definition for ‘na.omit’
.NSS.estimator: no visible global function definition for ‘resid’
NSrates: no visible global function definition for ‘time’
Nelson.Siegel: no visible global function definition for ‘optimize’
Srates: no visible global function definition for ‘time’
Svensson: no visible global function definition for ‘median’
Svensson: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  coef lm median na.omit optimize resid time
Consider adding
  importFrom("stats", "coef", "lm", "median", "na.omit", "optimize",
             "resid", "time")
to your NAMESPACE file.
Rd file 'ECBYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat.ECB, ECBYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

Rd file 'FedYieldCurve.Rd':
  \examples lines wider than 100 characters:
     plot(mat, FedYieldCurve[i,], type="o", xlab="Maturities structure in years", ylab="Interest rates values")

These lines will be truncated in the PDF manual.
kmeansN: no visible global function definition for ‘kmeans’
kmeansN: no visible global function definition for ‘aggregate’
kmeansN2: no visible global function definition for ‘aggregate’
kmeansN2: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  aggregate kmeans sd
Consider adding
  importFrom("stats", "aggregate", "kmeans", "sd")
to your NAMESPACE file.
'library' or 'require' call not declared from: ‘damr’
Deprecated license: CC BY-SA 2.0 + file LICENSE
Package suggested but not available for checking: ‘zdat’
Found the following apparent S3 methods exported but not registered:
  cbind.zoocat
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'merge':
  ‘cbind.zoocat’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: reshape2

Attaching package: 'zoocat'

The following object is masked from 'package:stats':

    cor

Quitting from lines 69-74 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
no applicable method for ‘cattr’ applied to an object of class "zoo"
Execution halted
.getPath: no visible global function definition for ‘predict’
ZIClass: no visible binding for global variable ‘na.omit’
ZIClass: no visible global function definition for ‘predict’
analyzeClass: no visible global function definition for ‘plot’
calibrate : findmax: no visible global function definition for ‘lowess’
calibrate: no visible global function definition for ‘lm’
calibrate: no visible global function definition for ‘anova’
calibrate: no visible global function definition for ‘coef’
focusGraph: no visible global function definition for ‘dev.list’
getTrain: no visible global function definition for ‘na.omit’
makeClass : selectVars: no visible global function definition for
  ‘as.formula’
predict.ZIClass: no visible global function definition for ‘predict’
processSampleAll: no visible global function definition for ‘predict’
viewResults: no visible global function definition for ‘par’
viewResults: no visible global function definition for ‘plot’
viewResults: no visible global function definition for ‘points’
viewResults: no visible global function definition for ‘text’
zidbDrawVignette: no visible global function definition for ‘dev.size’
zidbDrawVignette: no visible global function definition for ‘par’
zidbDrawVignette: no visible global function definition for ‘dev.cur’
zidbDrawVignette: no visible global function definition for
  ‘rasterImage’
zidbPlotNew: no visible global function definition for ‘par’
zidbPlotNew: no visible global function definition for ‘plot’
Undefined global functions or variables:
  anova as.formula coef dev.cur dev.list dev.size lm lowess na.omit par
  plot points predict rasterImage text
Consider adding
  importFrom("grDevices", "dev.cur", "dev.list", "dev.size")
  importFrom("graphics", "par", "plot", "points", "rasterImage", "text")
  importFrom("stats", "anova", "as.formula", "coef", "lm", "lowess",
             "na.omit", "predict")
to your NAMESPACE file.
File which contains pragma(s) suppressing diagnostics:
  ‘src/third_party/zstd-1.2.0/lib/dictBuilder/divsufsort.c’
Found the following apparent S3 methods exported but not registered:
  confint.zyp
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
confint.zyp: no visible global function definition for ‘qnorm’
confint.zyp: no visible global function definition for ‘var’
zyp.sen: no visible global function definition for ‘terms’
zyp.sen: no visible global function definition for ‘median’
zyp.trend.csv: no visible global function definition for ‘read.csv’
zyp.trend.csv: no visible global function definition for ‘write.csv’
zyp.yuepilon: no visible global function definition for ‘acf’
zyp.yuepilon: no visible binding for global variable ‘na.pass’
zyp.yuepilon: no visible global function definition for ‘confint’
zyp.yuepilon: no visible global function definition for ‘lm’
zyp.zhang: no visible global function definition for ‘acf’
zyp.zhang: no visible binding for global variable ‘na.pass’
zyp.zhang: no visible global function definition for ‘confint’
zyp.zhang: no visible global function definition for ‘lm’
Undefined global functions or variables:
  acf confint lm median na.pass qnorm read.csv terms var write.csv
Consider adding
  importFrom("stats", "acf", "confint", "lm", "median", "na.pass",
             "qnorm", "terms", "var")
  importFrom("utils", "read.csv", "write.csv")
to your NAMESPACE file.
Package required but not available: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mosaic’

Packages suggested but not available for checking:
  ‘car’ ‘ggplot2’ ‘HH’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GDINA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotly’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gsDesign’
Package required but not available: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘adephylo’
Packages required but not available: ‘ggplot2’ ‘dplyr’

Packages suggested but not available for checking:
  ‘pegas’ ‘hierfstat’ ‘poppr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘phylobase’ ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adephylo’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘adephylo’ ‘phylobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggplot2’
Running examples in ‘adklakedata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: adk_lake_shapes
> ### Title: Return path to Lake Polygons Shapefile
> ### Aliases: adk_lake_shapes
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.6.2, GDAL 2.2.4, proj.4 5.0.1
> bl = read_sf(adklakedata::adk_shape())
Error in read_sf(adklakedata::adk_shape()) : 
  package tibble not available: install first?
Execution halted
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ADM3.Rcheck/00install.out’ for details.
Packages required but not available: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking:
  ‘dynlm’ ‘forecast’ ‘rgl’ ‘sampleSelection’ ‘systemfit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘emmeans’ ‘lmerTest’ ‘car’

Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘klaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘AER’ ‘agricolae’ ‘broom’ ‘car’ ‘corrgram’ ‘dplyr’ ‘equivalence’
  ‘gge’ ‘ggplot2’ ‘HH’ ‘nullabor’ ‘qicharts’ ‘SpATS’
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crossa.wheat
> ### Title: Multi-environment trial of wheat for 18 genotypes at 25
> ###   locations
> ### Aliases: crossa.wheat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(crossa.wheat)
> dat <- crossa.wheat
> 
> # AMMI biplot.  Fig 3 of Crossa et al.
> if(require(agricolae)){
+   m1 <- with(dat, AMMI(E=loc, G=gen, R=1, Y=yield))
+   b1 <- m1$biplot[,1:4]
+   b1$PC1 <- -1 * b1$PC1 # Flip vertical
+   plot(b1$yield, b1$PC1, cex=0.0,
+        text(b1$yield, b1$PC1, cex=.5, labels=row.names(b1),col="brown"),
+        main="crossa.wheat AMMI biplot", xlab="Average yield", ylab="PC1", frame=TRUE)
+   mn <- mean(b1$yield)
+   abline(h=0, v=mn, col='wheat')
+ 
+   g1 <- subset(b1,type=="GEN")
+   text(g1$yield, g1$PC1, rownames(g1), col="darkgreen", cex=.5)
+ 
+   e1 <- subset(b1,type=="ENV")
+   arrows(mn, 0,
+          0.95*(e1$yield - mn) + mn, 0.95*e1$PC1,
+          col= "brown", lwd=1.8,length=0.1)
+ }
Loading required package: agricolae
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘agricolae’
> 
> # GGB example
> library(agridat)
> data(crossa.wheat)
> dat2 <- crossa.wheat
> 
> # FIXME: The loc grouping is now in the data
> 
> # Define mega-environment groups of locations
> dat2$eg <- ifelse(is.element(dat2$loc,
+                              c("KN","NB","PA","BJ","IL","TC",
+                                "JM","PI","AS","ID","SC","SS",
+                                "SJ","MS","MG","MM")), "Grp1", "Grp2")
> 
> library(gge)
Error in library(gge) : there is no package called ‘gge’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 44-53 (agridat_examples.Rmd) 
Error: processing vignette ‘agridat_examples.Rmd’ failed with diagnostics:
there is no package called 'gge'
Execution halted
Packages required but not available: ‘lmerTest’ ‘emmeans’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘data.tree’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘readr’ ‘readxl’

Packages suggested but not available for checking: ‘ggplot2’ ‘ggseas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘ggmcmc’ ‘hydroPSO’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 14-20 (V02.1_param_optim.Rmd) 
Error: processing vignette ‘V02.1_param_optim.Rmd’ failed with diagnostics:
there is no package called 'hydroPSO'
Execution halted
Packages suggested but not available for checking:
  ‘dplyr’ ‘ggplot2’ ‘tidyr’
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mpoly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplyr’
Error in re-building vignettes:
  ...
Quitting from lines 17-25 (alluvial.Rmd) 
Error: processing vignette ‘alluvial.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘alphahull’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘tidyquant’ ‘tidyverse’ ‘timetk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 26-29 (ameco_dataset.Rmd) 
Error: processing vignette ‘ameco_dataset.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package suggested but not available for checking: ‘Zelig’
Error in re-building vignettes:
  ...
Loading required package: Amelia
Loading required package: Rcpp
## 
## Amelia II: Multiple Imputation
## (Version 1.7.5, built: 2018-05-07)
## Copyright (C) 2005-2018 James Honaker, Gary King and Matthew Blackwell
## Refer to http://gking.harvard.edu/amelia/ for more information
## 
Loading required package: Zelig
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Zelig’

Error: processing vignette ‘amelia.Rnw’ failed with diagnostics:
 chunk 64 
Error in eval(expr, .GlobalEnv) : object ‘zls’ not found
Execution halted
Packages required but not available: ‘ggplot2’ ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘leaflet’ ‘purrr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘moveHMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Hmisc’
Packages required but not available: ‘vegan3d’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spbabel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ggmap’
Packages required but not available: ‘qdap’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgl’
Package required but not available: ‘vcfR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EnvStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘timetk’ ‘sweep’ ‘tibbletime’ ‘purrr’ ‘tibble’ ‘tidyr’
  ‘ggplot2’

Packages suggested but not available for checking: ‘tidyverse’ ‘tidyquant’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘caret’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DT’
Error in re-building vignettes:
  ...
Quitting from lines 39-73 (antaresH5.Rmd) 
Error: processing vignette ‘antaresH5.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Packages required but not available:
  ‘plotly’ ‘leaflet’ ‘geojsonio’ ‘leaflet.minicharts’

Package suggested but not available for checking: ‘rbokeh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘smacof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘shapes’ ‘rgl’ ‘depth’ ‘biclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotKML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’

Packages suggested but not available for checking: ‘afex’ ‘ez’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘broom’ ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘ez’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘apaTables’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pROC’
Error in re-building vignettes:
  ...
Quitting from lines 5-6 (./ch/glow.Rnw) 
Quitting from lines 8-8 (./ch/glow.Rnw) 
Error: processing vignette ‘aplore3-examples.Rnw’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Package suggested but not available for checking: ‘caret’
Running examples in ‘AppliedPredictiveModeling-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: concrete
> ### Title: Compressive Strength of Concrete from Yeh (1998)
> ### Aliases: concrete mixtures
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(concrete)
> 
> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Packages required but not available: ‘rms’ ‘shrink’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘brranching’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘erer’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: ‘soilDB’ ‘sharpshootR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ArchaeoPhases’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘hdrcde’ ‘DT’ ‘readr’ ‘ggthemes’ ‘ggplot2’ ‘ggalt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘archivist-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ahistory
> ### Title: Show Artifact's History
> ### Aliases: ahistory
> 
> ### ** Examples
> 
> 
> createLocalRepo("ahistory_check", default = TRUE)
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Package required but not available: ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Morpho’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘broom’ ‘pROC’
Running examples in ‘arsenal-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: modelsum
> ### Title: Fit models over each of a set of independent variables with a
> ###   response variable
> ### Aliases: modelsum modelsum print.modelsum print.modelsumList
> 
> ### ** Examples
> 
> 
> data(mockstudy)
> 
> tab1 <- modelsum(bmi ~ sex + age, data = mockstudy)
Error in loadNamespace(name) : there is no package called ‘broom’
Calls: modelsum ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘car’ ‘dplyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘lmerTest’ ‘phia’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘arulesViz’
Packages required but not available: ‘seriation’ ‘DT’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Hmisc’ ‘cacheSweave’
Packages required but not available: ‘readr’ ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘REBayes’ ‘Rmosek’
Error in re-building vignettes:
  ...
Quitting from lines 28-30 (adaptive_shrinkage.Rmd) 
Error: processing vignette ‘adaptive_shrinkage.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘llama’ ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dae’ ‘ggplot2’

Package which this enhances but not available for checking: ‘asreml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RVAideMemoire’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’

Package suggested but not available for checking: ‘klaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘haplo.stats’
Running examples in ‘asymLD-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compute.ALD
> ### Title: Compute ALD.
> ### Aliases: compute.ALD
> 
> ### ** Examples
> 
> library(asymLD)
> 
> # An example using haplotype frequencies from Wilson(2010)
> data(hla.freqs)
> hla.a_b <- hla.freqs[hla.freqs$locus1=="A" & hla.freqs$locus2=="B",]
> compute.ALD(hla.a_b)
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2       F.1    F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      A      B 0.1021811 0.340332 0.04876543 0.1903394 0.5150291 0.3857872
> hla.freqs$locus <- paste(hla.freqs$locus1, hla.freqs$locus2, sep="-")
> compute.ALD(hla.freqs[hla.freqs$locus=="C-B",])
   ALD.x.y is asymmetric LD for locus x conditioned on locus y

  locus1 locus2        F.1     F.1.2        F.2     F.2.1   ALD.1.2   ALD.2.1
1      C      B 0.08637241 0.7350216 0.05040254 0.4520268 0.8425979 0.6503396
> # Note: additonal columns on the input dataframe (e.g., "locus" above) are allowed, but
> # ignored by the function.
> 
> # An example using genotype data from the haplo.stats package
> require(haplo.stats)
Loading required package: haplo.stats
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘haplo.stats’
> data(hla.demo)
Warning in data(hla.demo) : data set ‘hla.demo’ not found
> geno <- hla.demo[,5:8]  #DPB-DPA
Error: object 'hla.demo' not found
Execution halted
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘purrr’ ‘tibble’

Packages suggested but not available for checking: ‘vdiffr’ ‘rfishbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘car’ ‘factoextra’ ‘GGally’ ‘ggplot2’ ‘ggrepel’ ‘plotROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘forecast’ ‘caret’
Running examples in ‘aurelius-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: extract_params.Arima
> ### Title: extract_params.Arima
> ### Aliases: extract_params.Arima
> 
> ### ** Examples
> 
> model <- stats::arima(presidents, c(3, 0, 0))
> extracted_model <- extract_params(model)
> 
> model <- forecast::Arima(USAccDeaths, order=c(2,2,2), seasonal=c(0,2,2))
Error in loadNamespace(name) : there is no package called ‘forecast’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘viridis’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘broom’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘ggfortify’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ijtiff’ ‘filesstrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidytext’ ‘purrr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 222-243 (full-example.Rmd) 
Error: processing vignette ‘full-example.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Package required but not available: ‘aws.alexa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RDAVIDWebService’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dlstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rpdb’ ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘janitor’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘keras’
Packages required but not available: ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesplot’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pegas’
Package required but not available: ‘ggplotify’

Packages suggested but not available for checking: ‘cowplot’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘tidyr’ ‘Lahman’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rmcfs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘GGally’ ‘dplyr’
Error in re-building vignettes:
  ...
Quitting from lines 271-275 (BAS-vignette.Rmd) 
Error: processing vignette ‘BAS-vignette.Rmd’ failed with diagnostics:
there is no package called 'GGally'
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tibble’
Packages required but not available:
  ‘Anthropometry’ ‘dplyr’ ‘ggplot2’ ‘ggthemes’ ‘hrbrthemes’ ‘purrr’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘bayesLife’ ‘bayesPop’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘heatmaply’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘doBy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggridges’

Packages suggested but not available for checking:
  ‘rstan’ ‘rstanarm’ ‘shinystan’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bayesLife’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘bartMachine’
Packages required but not available: ‘Luminescence’ ‘ArchaeoPhases’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘ggfortify’ ‘tibble’ ‘tidyr’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rms’ ‘ggplot2’ ‘Hmisc’
Packages required but not available: ‘RcmdrMisc’ ‘Rcmdr’ ‘car’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘biclust’
Running examples in ‘BcDiag-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: anomedOnlybic
> ### Title: The anomedOnlybic function
> ### Aliases: anomedOnlybic
> ### Keywords: anomedOnlybic
> 
> ### ** Examples
> 
> data(breastc)
> library(biclust)
Error in library(biclust) : there is no package called ‘biclust’
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘INLA’
Packages suggested but not available for checking: ‘bcmaps.rdata’ ‘ggplot2’
Packages required but not available: ‘taxize’ ‘treemap’ ‘ggplot2’

Package suggested but not available for checking: ‘rinat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘haven’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘beadarray’

Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tidyr’ ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 13-32 (belg1.Rmd) 
Error: processing vignette ‘belg1.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘benchmarkmeData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_datatable_past
> ### Title: Interactive table of results
> ### Aliases: get_datatable_past
> 
> ### ** Examples
> 
> ## Need the DT package
> ## View all results for prog test
> get_datatable_past("prog")
Warning: This function is deprecated and will be removed in the next version. 
              Instead, use https://jumpingrivers.shinyapps.io/benchmarkme/
Error in get_datatable_past("prog") : Install DT package to use datatable
Execution halted
Packages suggested but not available for checking: ‘DT’ ‘ggplot2’
Packages required but not available: ‘dplyr’ ‘readr’

Packages suggested but not available for checking: ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘LambertW’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘forecast’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘doBy’ ‘Hmisc’
Package required but not available: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘viridis’ ‘dendextend’ ‘biclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘factoextra’ ‘FactoMineR’ ‘ggplot2’ ‘ggrepel’ ‘rscopus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 25-34 (calibration.Rmd) 
Error: processing vignette ‘calibration.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking: ‘car’ ‘Hmisc’ ‘intsvy’
Package required but not available: ‘haplo.stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rgl’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Packages suggested but not available for checking: ‘dbplyr’ ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readxl’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘binom-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: binom.bayes
> ### Title: Binomial confidence intervals using Bayesian inference
> ### Aliases: binom.bayes binom.bayes.densityplot
> ### Keywords: univar htest models
> 
> ### ** Examples
> 
> # Example using highest probability density.
> hpd <- binom.bayes(
+   x = 0:10, n = 10, type = "highest", conf.level = 0.8, tol = 1e-9)
> print(hpd)
   method  x  n shape1 shape2       mean       lower     upper sig
1   bayes  0 10    0.5   10.5 0.04545455 0.000000000 0.0769566 0.2
2   bayes  1 10    1.5    9.5 0.13636364 0.003771457 0.2145408 0.2
3   bayes  2 10    2.5    8.5 0.22727273 0.053633312 0.3494770 0.2
4   bayes  3 10    3.5    7.5 0.31818182 0.127646004 0.4728042 0.2
5   bayes  4 10    4.5    6.5 0.40909091 0.214091147 0.5858428 0.2
6   bayes  5 10    5.5    5.5 0.50000000 0.309892028 0.6901080 0.2
7   bayes  6 10    6.5    4.5 0.59090909 0.414157185 0.7859089 0.2
8   bayes  7 10    7.5    3.5 0.68181818 0.527195809 0.8723540 0.2
9   bayes  8 10    8.5    2.5 0.77272727 0.650522982 0.9463667 0.2
10  bayes  9 10    9.5    1.5 0.86363636 0.785459228 0.9962285 0.2
11  bayes 10 10   10.5    0.5 0.95454545 0.923043403 1.0000000 0.2
> binom.bayes.densityplot(hpd)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
Error in binom.bayes.densityplot(hpd) : require(ggplot2) is not TRUE
Calls: binom.bayes.densityplot -> stopifnot
Execution halted
Packages required but not available: ‘rgl’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘reutils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 263-268 (biogas_quick_start.Rnw) 
Error: processing vignette ‘biogas_quick_start.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘phylobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘biogram-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.criterion_distribution
> ### Title: Plot criterion distribution
> ### Aliases: plot.criterion_distribution
> 
> ### ** Examples
> 
> target_feature <- create_feature_target(10, 375, 15, 600) 
> example_result <- distr_crit(target = target_feature[,1], 
+                              feature = target_feature[,2])
> plot(example_result)
> 
> # a ggplot2 plot
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: slam
Quitting from lines 16-40 (overview.Rmd) 
Error: processing vignette ‘overview.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘readr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘pROC’

Packages suggested but not available for checking:
  ‘Hmisc’ ‘ecospat’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bioinactivation’ ‘dplyr’ ‘ggplot2’ ‘MEIGOR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plsRcox’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 69-101 (bisect_vignette.Rmd) 
Error: processing vignette ‘bisect_vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘dplyr’ ‘readr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘ggExtra’
Error in re-building vignettes:
  ...
Quitting from lines 72-75 (Intro.Rmd) 
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘bnormnlr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bnlr
> ### Title: Bayesian Estimation for Normal Heteroscedastic Nonlinear
> ###   Regression Models.
> ### Aliases: bnlr
> 
> ### ** Examples
> 
> 
> ######################################################
> ###Simulation of heteroscedastic model, using gradient
> ######################################################
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Packages required but not available: ‘ggplot2’ ‘threejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘dplyr’
Error in re-building vignettes:
  ...
Quitting from lines 13-32 (bodenmiller.Rmd) 
Error: processing vignette ‘bodenmiller.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
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Packages suggested but not available for checking: ‘ggplot2’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘readxl’ ‘broom’ ‘tidyr’ ‘ggplot2’
  ‘ggfittext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘purrr’ ‘dplyr’ ‘rstan’ ‘tidyr’

Packages suggested but not available for checking:
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
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Quitting from lines 33-45 (the_bridgedist_basics.Rmd) 
Error: processing vignette ‘the_bridgedist_basics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rstan’ ‘rstanarm’
Error in re-building vignettes:
  ...
Loading required package: rjags
Loading required package: coda
Linked to JAGS 4.3.0
Loaded modules: basemod,bugs

Attaching package: 'R2jags'

The following object is masked from 'package:coda':

    traceplot

module glm loaded
Quitting from lines 51-95 (bridgesampling_example_stan.Rmd) 
Error: processing vignette ‘bridgesampling_example_stan.Rmd’ failed with diagnostics:
there is no package called 'rstan'
Execution halted
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  ‘ggplot2’ ‘rstan’ ‘bayesplot’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking:
  ‘Lahman’ ‘ggplot2’ ‘xergm’ ‘btergm’ ‘Hmisc’ ‘rstan’ ‘rstanarm’ ‘brms’
  ‘purrr’ ‘emmeans’ ‘AER’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
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Quitting from lines 24-36 (benchmarks.Rmd) 
Error: processing vignette ‘benchmarks.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking: ‘vsn’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  ‘ggplot2’ ‘dplyr’ ‘tidyr’
Packages required but not available: ‘diagis’ ‘ggplot2’

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-3>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <cancer>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <sessionInfo>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: gbm
Loading required package: survival
Loading required package: lattice
Loading required package: splines
Loading required package: parallel
Loaded gbm 2.1.3
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-3>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-4>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-5>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-6>
reason: Error in loadNamespace(name) : there is no package called 'formatR'


Error: processing vignette ‘pros.Rnw’ failed with diagnostics:
 chunk 2 
Error in library("pROC") : there is no package called 'pROC'
Execution halted
Package required but not available: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘recipes’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 11-14 (C5.0.Rmd) 
Error: processing vignette ‘C5.0.Rmd’ failed with diagnostics:
there is no package called 'recipes'
Execution halted
Package required but not available: ‘dynlm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  ‘smoof’ ‘car’ ‘dplyr’ ‘ggplot2’ ‘ggridges’
Error in re-building vignettes:
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Quitting from lines 47-69 (Adapting_Algorithm_for_CAISEr.Rmd) 
Error: processing vignette ‘Adapting_Algorithm_for_CAISEr.Rmd’ failed with diagnostics:
there is no package called 'smoof'
Execution halted
Packages required but not available: ‘ggplot2’ ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘taxize’ ‘ritis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘leaflet’ ‘readr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘systemfit’ ‘qvalue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘heplots’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qpcR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking: ‘pROC’ ‘klaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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Packages suggested but not available for checking: ‘klaR’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rio’

Packages suggested but not available for checking: ‘alr4’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: ‘expsmooth’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’

Package suggested but not available for checking: ‘GSIF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rms’
Packages required but not available: ‘ggplot2’ ‘tidyverse’ ‘dplyr’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ruv’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hypervolume’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘season’ ‘assertr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rms’ ‘CPE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyselect’

Packages suggested but not available for checking: ‘nycflights13’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘Hmisc’ ‘tidyr’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘caret’ ‘bartMachine’
Running ‘CBDA_test_training.R’ [2s/3s]
Running the tests in ‘tests/CBDA_test_training.R’ failed.
Complete output:
  > # Attach the CBDA library
  > suppressPackageStartupMessages(library(CBDA))
  > suppressPackageStartupMessages(library(randomForest ))
  > suppressPackageStartupMessages(library(glmnet ))
  > suppressPackageStartupMessages(library(SuperLearner))
  > suppressPackageStartupMessages(library(bartMachine))
  Error in library(bartMachine) : there is no package called 'bartMachine'
  Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 13-14 (cbsodataR.Rmd) 
Error: processing vignette ‘cbsodataR.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘readr’ ‘tibble’

Packages suggested but not available for checking: ‘leaflet’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GDINA’
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘broom’

Package suggested but not available for checking: ‘eemR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotly’ ‘freqparcoord’ ‘partools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘robustHD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ClusterR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’
Running examples in ‘censReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: censReg
> ### Title: Censored Regression (Tobit) Model
> ### Aliases: censReg print.censReg
> ### Keywords: models regression
> 
> ### ** Examples
> 
> ## Kleiber & Zeileis ( 2008 ), page 142
> data( "Affairs", package = "AER" )
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Running ‘censRegFail.R’ [1s/1s]
Running the tests in ‘tests/censRegFail.R’ failed.
Complete output:
  > library( "censReg" )
  Loading required package: maxLik
  Loading required package: miscTools
  
  Please cite the 'maxLik' package as:
  Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.
  
  If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
  https://r-forge.r-project.org/projects/maxlik/
  
  Please cite the 'censReg' package as:
  Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.
  
  If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
  https://r-forge.r-project.org/projects/sampleselection/
  > 
  > data( "Affairs", package = "AER" )
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'AER'
  Calls: data -> find.package
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Please cite the 'censReg' package as:
Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.

If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
https://r-forge.r-project.org/projects/sampleselection/

Error: processing vignette ‘censReg.Rnw’ failed with diagnostics:
 chunk 3 
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggrepel’
Error in re-building vignettes:
  ...
Quitting from lines 63-74 (Census2016.Rmd) 
Error: processing vignette ‘Census2016.Rmd’ failed with diagnostics:
object ‘.CensusDataTables’ not found
Execution halted
Package required but not available: ‘ggmap’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alr3’
Packages required but not available: ‘car’ ‘dplyr’ ‘ggplot2’ ‘tibble’

Package suggested but not available for checking: ‘productplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘systemfit’ ‘cplm’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘nonlinearTseries’
Packages required but not available: ‘rgl’ ‘ggplot2’ ‘sphereplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘tibble’
Running examples in ‘checkmate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkTibble
> ### Title: Check if an argument is a tibble
> ### Aliases: checkTibble check_tibble assertTibble assert_tibble testTibble
> ###   test_tibble expect_tibble
> 
> ### ** Examples
> 
> library(tibble)
Error in library(tibble) : there is no package called ‘tibble’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette ‘checkmate.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘pROC’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘seriation’ ‘rgl’ ‘speaq’
Running examples in ‘ChemoSpec-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmapSpectra
> ### Title: Seriated Heat Map for a Spectra Object
> ### Aliases: hmapSpectra
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> 
> data(SrE.IR)
> # Let's look just at the carbonyl region
> IR <- removeFreq(SrE.IR, rem.freq = SrE.IR$freq > 1850 | SrE.IR$freq < 1650)
> res <- hmapSpectra(IR, col = heat.colors(5), labCol = FALSE)
Error in hmapSpectra(IR, col = heat.colors(5), labCol = FALSE) : 
  You need to install package seriation to use this function
Execution halted
Packages required but not available: ‘dbplyr’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’ ‘purrr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘drc’ ‘qpcR’ ‘RDML’
Error in re-building vignettes:
  ...
Quitting from lines 13-46 (unstacking.bars.Rmd) 
Error: processing vignette ‘unstacking.bars.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘Hmisc’ ‘ggplot2’ ‘dplyr’ ‘ggmap’ ‘tigris’

Package suggested but not available for checking: ‘choroplethrAdmin1’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘stm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 21-92 (cifti_work.Rmd) 
Error: processing vignette ‘cifti_work.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages required but not available:
  ‘FactoMineR’ ‘factoextra’ ‘GGally’ ‘dendextend’ ‘viridis’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘userfriendlyscience’
Package suggested but not available for checking: ‘dendextend’
Running examples in ‘circlize-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: circos.dendrogram
> ### Title: Add circular dendrograms
> ### Aliases: circos.dendrogram
> 
> ### ** Examples
> 
> load(system.file(package = "circlize", "extdata", "bird.orders.RData"))
> 
> labels = hc$labels  # name of birds
> ct = cutree(hc, 6)  # cut tree into 6 pieces
> n = length(labels)  # number of bird species
> dend = as.dendrogram(hc)
> 
> circos.par(cell.padding = c(0, 0, 0, 0))
> circos.initialize(factors = "a", xlim = c(0, n)) # only one sector
> max_height = attr(dend, "height")  # maximum height of the trees
> circos.trackPlotRegion(ylim = c(0, 1), bg.border = NA, track.height = 0.3, 
+     panel.fun = function(x, y) {
+         for(i in seq_len(n)) {
+             circos.text(i-0.5, 0, labels[i], adj = c(0, 0.5), 
+                 facing = "clockwise", niceFacing = TRUE,
+                 col = ct[labels[i]], cex = 0.7)
+         }
+ })
> 
> suppressPackageStartupMessages(require(dendextend))
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dendextend’
> dend = color_branches(dend, k = 6, col = 1:6)
Error in color_branches(dend, k = 6, col = 1:6) : 
  could not find function "color_branches"
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘broom’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dataRetrieval’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dbplyr’ ‘feather’ ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘qualtRics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readxl’
Packages required but not available: ‘ggplot2’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘readtext’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(cld2)
  > 
  > test_check("cld2")
  ── 1. Error: vectorised input works (@test-detect.R#5)  ────────────────────────
  there is no package called 'readtext'
  1: library(readtext) at testthat/test-detect.R:5
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: vectorised input works (@test-detect.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘extRemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘xcms’ ‘CAMERA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘clubSandwich-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vcovCR.ivreg
> ### Title: Cluster-robust variance-covariance matrix for an ivreg object.
> ### Aliases: vcovCR.ivreg
> 
> ### ** Examples
> 
> library(AER)
Error in library(AER) : there is no package called ‘AER’
Execution halted
Running ‘testthat.R’ [190s/251s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clubSandwich)
  Registered S3 method overwritten by 'clubSandwich':
    method    from    
    bread.mlm sandwich
  > set.seed(20171124)
  > test_check("clubSandwich")
  ── 1. Error: (unknown) (@test_ivreg.R#3)  ──────────────────────────────────────
  there is no package called 'AER'
  1: library(AER, quietly = TRUE) at testthat/test_ivreg.R:3
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test_plm-first-differences.R#5)  ──────────────────────
  there is no package called 'AER'
  1: data(Fatalities, package = "AER") at testthat/test_plm-first-differences.R:5
  2: find.package(package, lib.loc, verbose = verbose)
  3: stop(gettextf("there is no package called %s", sQuote(pkg)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 593 SKIPPED: 5 FAILED: 2
  1. Error: (unknown) (@test_ivreg.R#3) 
  2. Error: (unknown) (@test_plm-first-differences.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘Hmisc’ ‘extracat’

Package suggested but not available for checking: ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘seriation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 37-42 (using-clusternomics.Rmd) 
Error: processing vignette ‘using-clusternomics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘car’ ‘data.tree’ ‘dendextend’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WeightedCluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’ ‘dplyr’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggraph’ ‘dplyr’ ‘ggplot2’ ‘viridis’

Package suggested but not available for checking: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘VarSelLCM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘smoof’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forcats’ ‘tidyr’ ‘purrr’ ‘dplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggstance’

Package suggested but not available for checking: ‘WeightIt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘likert’ ‘dplyr’ ‘tidyr’ ‘skimr’ ‘DT’ ‘haven’ ‘readr’
  ‘tibble’ ‘purrr’ ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readr’ ‘usethis’ ‘tibble’ ‘purrr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘car’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 19-30 (codingMatrices.Rnw) 
Error: processing vignette ‘codingMatrices.Rnw’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 110-112 (Temporal_Diversity_Indices.Rmd) 
Error: processing vignette ‘Temporal_Diversity_Indices.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘useful’ ‘dplyr’ ‘tibble’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘haplo.stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘data.tree’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘purrrlyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘clusterSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘backShift’
Packages required but not available: ‘Hmisc’ ‘SNPassoc’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GEOquery’

Packages suggested but not available for checking: ‘inSilicoDb’ ‘GEOmetadb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘nonparaeff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Packages suggested but not available for checking: ‘ggplot2’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rminer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bigrquery’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘hdrcde’ ‘DendSer’
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘alphahull’
Error in re-building vignettes:
  ...
Quitting from lines 239-240 (my-vignette.Rmd) 
Error: processing vignette ‘my-vignette.Rmd’ failed with diagnostics:
The package alpha.hull is required for this procedure, please install it
Execution halted
Packages required but not available: ‘readxl’ ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘contoureR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contourLinesR
> ### Title: Get Contour Lines (list)
> ### Aliases: contourLinesR
> 
> ### ** Examples
> 
> library(contoureR)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘rms’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  date.cpp:173:53: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ConvCalendar.Rcheck/00install.out’ for details.
Package required but not available: ‘gsDesign’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘ggplot2’

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘quanteda’
Package suggested but not available for checking: ‘quanteda’
Running examples in ‘corpustools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tCorpus$top_features
> ### Title: Show top features
> ### Aliases: tCorpus$top_features top_features
> 
> ### ** Examples
> 
> tc = tokens_to_tcorpus(corenlp_tokens, token_id_col = 'id')
> 
> tc$top_features('lemma')
Error in loadNamespace(name) : there is no package called ‘reshape2’
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘missMDA’
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘seriation’ ‘purrr’ ‘tibble’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘forecast’ ‘hts’
Packages required but not available: ‘cosinor’ ‘ggplot2’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dataRetrieval’ ‘dplyr’ ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘hurricaneexposure’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘choroplethr’ ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggmap’ ‘ggplot2’ ‘purrr’ ‘rnoaa’ ‘tibble’ ‘tidyr’ ‘tigris’

Package suggested but not available for checking: ‘countytimezones’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘bartMachine’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘vdiffr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qvalue’
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘rgl’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘UpSetR’ ‘dplyr’ ‘ggplot2’ ‘ggridges’ ‘tidyr’ ‘purrr’
  ‘clusterProfiler’

Packages suggested but not available for checking: ‘dbplyr’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rcrossref’
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggmcmc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nbpMatching’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tables’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘haven’ ‘labelled’ ‘readr’ ‘readxl’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gutenbergr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tidytext’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘adabag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘haven’
Packages required but not available: ‘ggplot2’ ‘qte’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FactoMineR’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 38-45 (csp.Rmd) 
Error: processing vignette ‘csp.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/cstab.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘readr’
Package suggested but not available for checking: ‘crawl’
Error in re-building vignettes:
  ...
Quitting from lines 36-71 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘tea’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 12-17 (cubist.Rmd) 
Error: processing vignette ‘cubist.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Packages required but not available: ‘feature’ ‘hdrcde’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘tibble’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tableone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘ggbeeswarm’
Error in re-building vignettes:
  ...
Quitting from lines 110-118 (how_to_test_CVs.Rmd) 
Error: processing vignette ‘how_to_test_CVs.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘cvxclustr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cvxclust
> ### Title: Convex Clustering Path via Variable Splitting Methods
> ### Aliases: cvxclust
> 
> ### ** Examples
> 
> ## Clusterpaths for Mammal Dentition
> data(mammals)
> X <- as.matrix(mammals[,-1])
> X <- t(scale(X,center=TRUE,scale=FALSE))
> n <- ncol(X)
> 
> ## Pick some weights and a sequence of regularization parameters.
> k <- 5
> phi <- 0.5
> w <- kernel_weights(X,phi)
> w <- knn_weights(w,k,n)
> gamma <- seq(0.0,43, length.out=100)
> 
> ## Perform clustering
> sol <- cvxclust(X,w,gamma)
Warning in cvxclust_ama(X, Lambda, ix - 1, M1 - 1, M2 - 1, s1, s2, w[w >  :
  The stepsize nu may be too large. Setting it to maximum of 1/n and 1/AnM.
> 
> ## Plot the cluster path
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package suggested but not available for checking: ‘leaflet’
Error in re-building vignettes:
  ...
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette ‘cycling_data_analysis.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘caret’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘dbplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘purrr’

Package which this enhances but not available for checking: ‘treemap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘d3r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘pdp’ ‘ggplot2’ ‘breakDown’ ‘factorMerger’ ‘ggpubr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggmcmc’

Packages suggested but not available for checking: ‘ggplot2’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: dams
Loading required package: ggplot2
Loading required package: maps
Loading required package: mapproj
Quitting from lines 67-71 (dams.Rmd) 
Error: processing vignette ‘dams.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Packages required but not available:
  ‘adegenet’ ‘tidyr’ ‘ggplot2’ ‘rgl’ ‘pca3d’ ‘pegas’ ‘SNPassoc’
  ‘StAMPP’ ‘qvalue’ ‘plotly’

Packages suggested but not available for checking: ‘mmod’ ‘PopGenReport’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/DatABEL.Rcheck/00install.out’ for details.
Package required but not available: ‘GeneralizedUmatrix’

Packages suggested but not available for checking:
  ‘DataVisualizations’ ‘AdaptGauss’ ‘rgl’ ‘ProjectionBasedClustering’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘nycflights13’ ‘tibble’
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘Rhipe’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-72 (get_started.Rmd) 
Error: processing vignette ‘get_started.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kableExtra’
Error in re-building vignettes:
  ...
Loading required package: lubridate

Attaching package: 'lubridate'

The following object is masked from 'package:base':

    date

Loading required package: stringr
Loading required package: Matrix
Loading required package: progress
dataPreparation 0.3.6
Type dataPrepNews() to see new features/changes/bug fixes.

Attaching package: 'data.table'

The following objects are masked from 'package:lubridate':

    hour, isoweek, mday, minute, month, quarter, second, wday,
    week, yday, year

Quitting from lines 16-54 (dataPreparation.Rmd) 
Error: processing vignette ‘dataPreparation.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Packages suggested but not available for checking:
  ‘car’ ‘doBy’ ‘ggplot2’ ‘colormap’

VignetteBuilder packages required for checking but not installed:
  ‘car’ ‘doBy’ ‘ggplot2’ ‘colormap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DiagrammeR’

Package suggested but not available for checking: ‘treemap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘AdaptGauss’ ‘ggplot2’

Packages suggested but not available for checking:
  ‘plotly’ ‘ggmap’ ‘rgl’ ‘choroplethr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dwapi’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SASxport’
Packages required but not available: ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘seqHMM’ ‘TraMineR’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SDD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘purrr’

Packages suggested but not available for checking: ‘dbplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking: ‘Lahman’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘dplyr’ ‘ggplot2’ ‘readr’

Package suggested but not available for checking: ‘ggExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘chillR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘DT’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 49-59 (RC_units.Rmd) 
Error: processing vignette ‘RC_units.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘PSF’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘cowplot’ ‘ggplot2’
Package required but not available: ‘Deducer’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Deducer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Deducer’ ‘klaR’

Depends: includes the non-default packages:
  ‘Deducer’ ‘psych’ ‘GPArotation’ ‘mvnormtest’ ‘irr’ ‘klaR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘car’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Deducer’ ‘OpenStreetMap’ ‘Hmisc’

Depends: includes the non-default packages:
  ‘JavaGD’ ‘Deducer’ ‘sp’ ‘maptools’ ‘OpenStreetMap’ ‘scales’ ‘rgdal’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘SASxport’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 115-125 (ODE_parameter_inference.Rmd) 
Error: processing vignette ‘ODE_parameter_inference.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘DiagrammeR’
Packages required but not available: ‘forecast’ ‘ftsa’ ‘rainbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking:
  ‘seriation’ ‘heatmaply’ ‘d3heatmap’ ‘DendSer’

Packages which this enhances but not available for checking:
  ‘ggdendro’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘seriation’ ‘gapmap’
Error in re-building vignettes:
  ...
Quitting from lines 27-32 (example_figures.Rmd) 
Error: processing vignette ‘example_figures.Rmd’ failed with diagnostics:
there is no package called 'seriation'
Execution halted
Packages required but not available: ‘ggplot2’ ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FactoMineR’

Package suggested but not available for checking: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘rgl’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘haven’ ‘readr’ ‘readxl’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘ijtiff’ ‘autothresholdr’ ‘filesstrings’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘tibble’ ‘DT’ ‘purrr’ ‘dplyr’ ‘dbplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MLInterfaces’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WGCNA’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘MEGENA’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘DiceDesign-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rss3d
> ### Title: 3D graphical tool for defect detection of Space-Filling Designs.
> ### Aliases: rss3d
> ### Keywords: design
> 
> ### ** Examples
> 
> 	# An orthogonal array in 3D   
> data(OA131)
> 
> 	# centering the design points of this 7-levels design
> OA <- (OA131 + 0.5)/7
> 
> 	# 2D projections onto coordinate axis 
> pairs(OA, xlim=c(0,1), ylim=c(0,1))
> 	# Now let us look at the 3D properties with the 3D RSS (requires the rgl package)
> rss <- rss3d(OA, lower=c(0,0,0), upper=c(1,1,1))

3D Radial Scanning Statistic (RSS) with GREENWOOD statistic
Discretization step (in degree) : 3

Maximum of RS statistic values (global statistic) per triplet of dimensions
(1,2,3) 0.2621302

[1] "Error : the package rgl is not installed"
Error in rss3d(OA, lower = c(0, 0, 0), upper = c(1, 1, 1)) : 
  object 'dir.max' not found
Execution halted
Package suggested but not available for checking: ‘GPareto’
Packages required but not available:
  ‘caret’ ‘dplyr’ ‘ggplot2’ ‘Hmisc’ ‘klaR’ ‘largeVis’ ‘NMF’ ‘purrr’
  ‘quantable’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘dielectric-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AgPalik
> ### Title: AgPalik
> ### Aliases: AgPalik
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(AgPalik)
> str(AgPalik$raw())
'data.frame':	241 obs. of  4 variables:
 $ wavelength: num  0.155 0.207 0.248 0.275 0.31 ...
 $ epsilon   : cplx  1+0i 1+0i 1+0i ...
 $ real      : num  1 1 1 1 1.01 ...
 $ imag      : num  5.84e-06 1.68e-05 3.04e-05 4.42e-05 7.16e-05 ...
> AgPalik$comment
$source
[1] "Silver in the visible, Palik"

$units
[1] "nanometres"

> demo(AgPalik)


	demo(AgPalik)
	---- ~~~~~~~

> library(dielectric)

> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Calls: demo -> source -> withVisible -> eval -> eval -> library
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking: ‘purrr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘missMethyl’ ‘methylumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘diffrprojects’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘systemfit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Packages suggested but not available for checking:
  ‘DiffusionRgqd’ ‘DiffusionRjgqd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘DiffusionRgqd’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘rgl’ ‘tidyr’
Running examples in ‘dimRed-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_R_NX
> ### Title: plot_R_NX
> ### Aliases: plot_R_NX
> 
> ### ** Examples
> 
> 
> ## define which methods to apply
> embed_methods <- c("Isomap", "PCA")
> ## load test data set
> data_set <- loadDataSet("3D S Curve", n = 1000)
> ## apply dimensionality reduction
> data_emb <- lapply(embed_methods, function(x) embed(data_set, x))
2018-05-23 05:19:07: Isomap START
2018-05-23 05:19:07: constructing knn graph
2018-05-23 05:19:07: calculating geodesic distances
2018-05-23 05:19:08: cmdscale
2018-05-23 05:19:10: post processing
> names(data_emb) <- embed_methods
> ## plot the R_NX curves:
> plot_R_NX(data_emb) +
+     ggplot2::theme(legend.title = ggplot2::element_blank(),
+                    legend.position = c(0.5, 0.1),
+                    legend.justification = c(0.5, 0.1))
Error in chckpkg("ggplot2") : 
  require 'ggplot2' package, install it using install.packages('ggplot2')
Calls: plot_R_NX -> chckpkg
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 12-17 (DirectEffects.Rmd) 
Error: processing vignette ‘DirectEffects.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘alphahull’
Running ‘ggplot.R’ [0s/1s]
  Running ‘lasso.R’ [0s/1s]
Running the tests in ‘tests/lasso.R’ failed.
Complete output:
  > library(directlabels)
  > data(prostate,package="ElemStatLearn")
  > pros <- subset(prostate,select=-train,train==TRUE)
  > ycol <- which(names(pros)=="lpsa")
  > x <- as.matrix(pros[-ycol])
  > y <- pros[[ycol]]
  > library(lars)
  Loaded lars 1.2
  
  > fit <- lars(x,y,type="lasso")
  > beta <- scale(coef(fit),FALSE,1/fit$normx)
  > 
  > ## Degenerate case: one 0 curves.
  > beta[, "gleason"] <- 0
  > arclength <- rowSums(abs(beta))
  > path <- data.frame(
  +   step=as.integer(row(beta)),
  +   variable=colnames(beta)[as.integer(col(beta))],
  +   arclength=arclength[as.integer(row(beta))],
  +   standardized.coef=as.numeric(beta))
  > library(ggplot2)
  Error in library(ggplot2) : there is no package called 'ggplot2'
  Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘tidyr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggdendro’ ‘seriation’
Package suggested but not available for checking: ‘FactoMineR’
Packages suggested but not available for checking: ‘caret’ ‘pec’
Running examples in ‘discSurv-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aucUno
> ### Title: Area under the Curve Estimation
> ### Aliases: aucUno
> ### Keywords: survival
> 
> ### ** Examples
> 
> #####################################################
> # Example with cross validation and unemployment data 
> 
> library(Ecdat)
Loading required package: Ecfun

Attaching package: ‘Ecfun’

The following object is masked from ‘package:base’:

    sign


Attaching package: ‘Ecdat’

The following object is masked from ‘package:datasets’:

    Orange

> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Running ‘UnitTestsDiscSurvDataTransform.R’ [2s/4s]
  Running ‘UnitTestsDiscSurvEstimation.R’ [2s/3s]
  Running ‘UnitTestsDiscSurvEvalShort.R’ [4s/6s]
  Running ‘UnitTestsDiscSurvEvaluation.R’ [2s/2s]
Running the tests in ‘tests/UnitTestsDiscSurvEvaluation.R’ failed.
Complete output:
  > library(discSurv)
  > library(pec)
  Error in library(pec) : there is no package called 'pec'
  Execution halted
Packages required but not available: ‘caret’ ‘dplyr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘qpcR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dynlm’ ‘AER’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘RcmdrMisc’ ‘purrr’ ‘tibble’ ‘tidyselect’
  ‘kableExtra’

Package suggested but not available for checking: ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘purrr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘purrr’
Error in re-building vignettes:
  ...
Quitting from lines 330-331 (dosresmeta.Rnw) 
Error: processing vignette ‘dosresmeta.Rnw’ failed with diagnostics:
there is no package called 'rms'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘broom’ ‘dplyr’ ‘ggstance’ ‘purrr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rgbif’
Packages required but not available: ‘qpcR’ ‘readxl’

Packages suggested but not available for checking: ‘DT’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘forecast’
Packages required but not available: ‘tidyverse’ ‘tidyr’ ‘DT’

Package suggested but not available for checking: ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking:
  ‘dbplyr’ ‘dtplyr’ ‘ggplot2’ ‘Lahman’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dbplyr’ ‘dplyr’ ‘purrr’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘drc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking: ‘DT’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘BIGL’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid NAMESPACE file, parsing gives:
Error in utils::packageVersion("dplyr"): package ‘dplyr’ not found

See section ‘Package namespaces’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘crosstalk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Package suggested but not available for checking: ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggrepel’

Packages suggested but not available for checking: ‘TSclust’ ‘TSdist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘frailtyEM’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rms’ ‘plotly’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘DataCombine’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘TraMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘DT’ ‘leaflet’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘vdiffr’ ‘incidence’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(earlyR)
  > 
  > test_check("earlyR")
  Error in library(incidence) : there is no package called 'incidence'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 25-28 (ebayesthresh.Rmd) 
Error: processing vignette ‘ebayesthresh.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 29-31 (ecb_sdw.Rmd) 
Error: processing vignette ‘ecb_sdw.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggmap’ ‘ggrepel’ ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘WGCNA’

Packages suggested but not available for checking:
  ‘factoextra’ ‘viridis’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘d3heatmap’ ‘ggplot2’ ‘plotly’

Package suggested but not available for checking: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘vdiffr’
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘Hmisc’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dae’ ‘emmeans’ ‘ggplot2’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bupaR’ ‘dplyr’ ‘ggplot2’ ‘ggthemes’ ‘tibble’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘purrr’ ‘dplyr’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 12-18 (edgarWebR.Rmd) 
Error: processing vignette ‘edgarWebR.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘DT’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  newmat5.cpp:494:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/EditImputeCont.Rcheck/00install.out’ for details.
Packages required but not available: ‘haven’ ‘tibble’ ‘readr’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘tidyr’ ‘plotly’ ‘ggthemes’ ‘rmapshaper’

Packages suggested but not available for checking:
  ‘purrr’ ‘purrrlyr’ ‘GGally’ ‘broom’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘viridis’

Packages suggested but not available for checking:
  ‘cdom’ ‘ggplot2’ ‘tidyr’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘viridis’

Packages suggested but not available for checking: ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘heplots’ ‘car’
Packages required but not available: ‘readr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Package suggested but not available for checking: ‘eggCountsExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘btergm’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EGRET’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dataRetrieval’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ei-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tomogRxC3d
> ### Title: Plotting 2x3 Ecological Inference Estimates in 3 dimensions
> ### Aliases: tomogRxC3d
> 
> ### ** Examples
> 
> data(RxCdata)
> formula <- cbind(turnout, noturnout) ~ cbind(white, black, hisp)
> tomogRxC3d(formula, RxCdata, total=NULL, lci=TRUE, estimates=TRUE, ci=TRUE, transparency=.5, 
+ 	light=FALSE, rotate=FALSE)
Error: Package rgl is needed for the tomogRxC3d function to work. Please install it.
Execution halted
Package required but not available: ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘readODS’ ‘readxl’ ‘EnvStats’ ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘prim’
Package required but not available: ‘iCheck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘elrm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.elrm
> ### Title: Plot Diagnostics for an elrm Object
> ### Aliases: plot.elrm
> ### Keywords: methods
> 
> ### ** Examples
> 
> # Drug dataset example with sex and treatment as the variables of interest
> data(drugDat);
> drug.elrm = elrm(formula=recovered/n~sex+treatment, interest=~sex+treatment, r=4, 
+ 	iter=50000, burnIn=1000, dataset=drugDat);
Generating the Markov chain ...
Progress:   0%  Progress:   5%  Progress:  10%  Progress:  15%  Progress:  20%  Progress:  25%  Progress:  30%  Progress:  35%  Progress:  40%  Progress:  45%  Progress:  50%  Progress:  55%  Progress:  60%  Progress:  65%  Progress:  70%  Progress:  75%  Progress:  80%  Progress:  85%  Progress:  90%  Progress:  95%  Progress: 100%  
Generation of the Markov Chain required 4 secs
Conducting inference ...
Inference required 1 secs
> 
> # Plot the sampled values of the sufficient statistic for each parameter of 
> # interest (sex and treatment)
> plot(drug.elrm,p=0.5,ask=TRUE);
Error in plot.default(drug.elrm, p = 0.5, ask = TRUE) : 
  argument 2 matches multiple formal arguments
Calls: plot
Execution halted
Package required but not available: ‘FactoMineR’

Packages suggested but not available for checking: ‘lumi’ ‘vsn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘DataCombine’ ‘ggplot2’ ‘lmerTest’ ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘HLMdiag’ ‘readODS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking: ‘caret’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘bayesplot’ ‘brms’ ‘car’ ‘mediation’ ‘lmerTest’

Packages which this enhances but not available for checking:
  ‘glmmADMB’ ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘purrr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘robustHD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spocc’
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-69 (GLMs.Rmd) 
Error: processing vignette ‘GLMs.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dendextend’ ‘ggplot2’ ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘EnsembleBase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘drc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘xcms’ ‘MSnbase’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘epade-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: box.plot.wtd
> ### Title: weighted Boxplot
> ### Aliases: box.plot.wtd
> ### Keywords: boxplot
> 
> ### ** Examples
> 
> x<-rnorm(1000)
> g<-round(runif(1000))
> w<-abs(rnorm(1000))
> d<- data.frame(x, g, w)
> box.plot.wtd('x', 'g', w='w', data=d)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Calls: box.plot.wtd -> library
Execution halted
Package required but not available: ‘timeROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘threejs’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘dplyr’ ‘tidyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kableExtra’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘incidence’
Error in re-building vignettes:
  ...
Quitting from lines 122-133 (epitrix.Rmd) 
Error: processing vignette ‘epitrix.Rmd’ failed with diagnostics:
there is no package called 'incidence'
Execution halted
Package required but not available: ‘PairedData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘car’ ‘broom’ ‘dplyr’ ‘modelr’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readODS’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘sjmisc’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘haven’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘readr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘brms’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AER’

Package which this enhances but not available for checking: ‘broom’
Running ‘sleep.R’ [0s/1s]
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [20s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Error: vcov works (@test-s3-methods.R#232)  ──────────────────────────────
  there is no package called 'AER'
  1: library(AER) at testthat/test-s3-methods.R:232
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 372 SKIPPED: 6 FAILED: 1
  1. Error: vcov works (@test-s3-methods.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’

Packages suggested but not available for checking:
  ‘dbplyr’ ‘macleish’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’

Packages suggested but not available for checking: ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’ ‘readr’
Packages required but not available:
  ‘dplyr’ ‘broom’ ‘tibble’ ‘tidyr’ ‘readr’

Packages suggested but not available for checking: ‘ggplot2’ ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘readr’ ‘readxl’ ‘tibble’ ‘tidyr’ ‘viridis’

Packages suggested but not available for checking:
  ‘DT’ ‘ggalt’ ‘forcats’ ‘statip’ ‘purrrlyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyquant’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘geomorph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rrepast’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘filesstrings’ ‘styler’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘Hmisc’ ‘tidyr’ ‘dplyr’ ‘ggplot2’ ‘DT’ ‘kableExtra’

Packages suggested but not available for checking:
  ‘gapminder’ ‘tidyquant’ ‘wbstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘phylobase’
Package suggested but not available for checking: ‘smoof’
Packages required but not available: ‘DT’ ‘dplyr’ ‘tidyr’ ‘ggplot2’

Packages suggested but not available for checking: ‘FactoMineR’ ‘GDAtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘GEOquery’ ‘propr’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 57-64 (labels-support.Rmd) 
Error: processing vignette ‘labels-support.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  ‘dplyr’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘broom’ ‘ggplot2’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘drc’ ‘dplyr’

Package suggested but not available for checking: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘refund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dendextend’ ‘FactoMineR’ ‘ggpubr’ ‘ggrepel’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘ggpubr’ ‘agricolae’ ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘FactoMineR’ ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘OpenML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘FactoClass’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidygraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggformula’ ‘mosaic’ ‘ggplot2’ ‘dplyr’

Packages suggested but not available for checking:
  ‘mosaicCalc’ ‘tidyr’ ‘readr’ ‘Hmisc’ ‘car’ ‘alr3’ ‘corrgram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mosaic’ ‘mosaicCalc’

Packages suggested but not available for checking:
  ‘Hmisc’ ‘car’ ‘alr3’ ‘corrgram’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Packages required but not available: ‘DESeq2’ ‘destiny’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘face’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘fdapace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘doBy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘plot3Drgl’ ‘rgl’
Packages suggested but not available for checking: ‘ggplot2’ ‘refund’
Package suggested but not available for checking: ‘fds’
Running examples in ‘fdcov-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: classifier-com
> ### Title: Functional data classifier via concentration inequalities
> ### Aliases: classifier-com classif.com predict.classif.com
> 
> ### ** Examples
> 
> ## Not run: 
> ##D  library(fds);
> ##D  # Setup training data
> ##D  dat1 = rbind( 
> ##D    t(aa$y[,1:100]), t(ao$y[,1:100]), t(dcl$y[,1:100]), 
> ##D    t(iy$y[,1:100]), t(sh$y[,1:100]) 
> ##D  );
> ##D  # Setup testing data
> ##D  dat2 = rbind( 
> ##D    t(aa$y[,101:400]), t(ao$y[,101:400]), t(dcl$y[,101:400]), 
> ##D    t(iy$y[,101:400]), t(sh$y[,101:400]) 
> ##D  );
> ##D  
> ##D  datgrp = gl(5,100);
> ##D  clCom = classif.com( datgrp, dat1 );
> ##D  grp = predict( clCom, dat2, LOADING=TRUE );
> ##D  acc = c(
> ##D    sum( grp[1:300]==1 ), sum( grp[301:600]==2 ), sum( grp[601:900]==3 ), 
> ##D    sum( grp[901:1200]==4 ), sum( grp[1201:1500]==5 )
> ##D  )/300;
> ##D  print(rbind(gl(5,1),signif(acc,3)));
> ## End(Not run)
> ## Don't show: 
>  library(fds);
Error in library(fds) : there is no package called ‘fds’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 29-41 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'fds'
Execution halted
Packages required but not available: ‘Fgmutils’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mosaic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rainbow’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘cellranger’ ‘dplyr’ ‘googlesheets’ ‘readr’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘soilDB’ ‘Hmisc’ ‘readr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plotKML’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘FField-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FField-package
> ### Title: Force field simulation for a set of points
> ### Aliases: FField FField-package
> ### Keywords: package
> 
> ### ** Examples
> 
> # Repel points
> coords <-
+   FFieldPtRep(coords = cbind(mtcars$wt * 100 / max(mtcars$wt), 
+                              mtcars$mpg * 100 / max(mtcars$mpg)),
+               rep.fact = 40)
> head(mtcars)
                   mpg cyl disp  hp drat    wt  qsec vs am gear carb
Mazda RX4         21.0   6  160 110 3.90 2.620 16.46  0  1    4    4
Mazda RX4 Wag     21.0   6  160 110 3.90 2.875 17.02  0  1    4    4
Datsun 710        22.8   4  108  93 3.85 2.320 18.61  1  1    4    1
Hornet 4 Drive    21.4   6  258 110 3.08 3.215 19.44  1  0    3    1
Hornet Sportabout 18.7   8  360 175 3.15 3.440 17.02  0  0    3    2
Valiant           18.1   6  225 105 2.76 3.460 20.22  1  0    3    1
> head(coords)
         x        y
1 45.11259 58.47014
2 54.19136 61.20140
3 40.34714 69.42976
4 62.48920 65.94822
5 59.81417 56.33633
6 66.54832 53.33343
>   
> # Demo
> FFieldPtRepDemo()
Error in library(ggplot2) : there is no package called ‘ggplot2’
Calls: FFieldPtRepDemo -> library
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘dplyr’ ‘colorplaner’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(fiftystater)
  > 
  > test_check("fiftystater")
  ── 1. Error: (unknown) (@test_fifty_states.R#1)  ───────────────────────────────
  there is no package called 'ggplot2'
  1: library(ggplot2) at testthat/test_fifty_states.R:1
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_fifty_states.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 54-76 (fiftystater.Rmd) 
Error: processing vignette ‘fiftystater.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘tibble’ ‘datadr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘purrr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘diveRsity’
Packages required but not available:
  ‘klaR’ ‘ggplot2’ ‘GGally’ ‘Rcmdr’ ‘rgl’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘DT’ ‘purrr’ ‘readr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 24-29 (Using_fishdata.Rmd) 
Error: processing vignette ‘Using_fishdata.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggthemes’
Packages required but not available: ‘DT’ ‘dplyr’

Packages suggested but not available for checking:
  ‘EnvStats’ ‘ExtDist’ ‘revdbayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tidyverse’ ‘broom’ ‘tidytext’ ‘ggthemes’ ‘ggraph’ ‘highcharter’
  ‘janitor’
Running examples in ‘fivethirtyeight-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ahca_polls
> ### Title: American Health Care Act Polls
> ### Aliases: ahca_polls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # To convert data frame to tidy data (long) format, run:
> library(tidyverse)
Error in library(tidyverse) : there is no package called ‘tidyverse’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 19-30 (bechdel.Rmd) 
Error: processing vignette ‘bechdel.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Packages required but not available: ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘plotly’ ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘seriation’
Package required but not available: ‘ContaminatedMixt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggsn’ ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘multipanelfigure’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘flowWorkspace’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘LogConcDEAD’
Error in re-building vignettes:
  ...
Quitting from lines 127-133 (documentation.Rmd) 
Error: processing vignette ‘documentation.Rmd’ failed with diagnostics:
there is no package called 'LogConcDEAD'
Execution halted
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘metaplot’

Package suggested but not available for checking: ‘wrangle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘hrbrthemes’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘dtplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘expsmooth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘broom’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘homals’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(formattable)
  > 
  > test_check("formattable")
  Failed with error:  'there is no package called 'DT''
  ── 1. Error: as.datatable (@test-render.R#18)  ─────────────────────────────────
  requireNamespace("DT") is not TRUE
  1: as.datatable(f) at testthat/test-render.R:18
  2: as.datatable.formattable(f)
  3: stopifnot(is.formattable(x), requireNamespace("DT"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 257 SKIPPED: 1 FAILED: 1
  1. Error: as.datatable (@test-render.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Failed with error:  'there is no package called 'DT''
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette ‘formattable-data-frame.Rmd’ failed with diagnostics:
requireNamespace("DT") is not TRUE
Execution halted
Package required but not available: ‘recipes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘FactoMineR’ ‘forcats’ ‘ggplot2’ ‘likert’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 23-31 (Overview.Rmd) 
Error: processing vignette ‘Overview.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 50-83 (fourierin_details.Rmd) 
Error: processing vignette ‘fourierin_details.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘mvoutlier’
Packages required but not available: ‘ggplot2’ ‘forecast’ ‘fma’ ‘expsmooth’

Packages suggested but not available for checking:
  ‘GGally’ ‘Mcomp’ ‘purrr’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘fma’ ‘expsmooth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘fractional-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: numerical
> ### Title: Convert a fractional object to the equivalent numeric object
> ### Aliases: numerical numerical.charFrac numerical.default
> ###   numerical.fractional
> 
> ### ** Examples
> 
> suppressPackageStartupMessages(library(dplyr))
Error in library(dplyr) : there is no package called ‘dplyr’
Calls: suppressPackageStartupMessages -> withCallingHandlers -> library
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 18-26 (Theory.Rmd) 
Error: processing vignette ‘Theory.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘ggplot2’ ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘plotly’ ‘egg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Loading required package: oro.nifti
oro.nifti 0.9.1
Quitting from lines 14-29 (exploring_included_data.Rmd) 
Error: processing vignette ‘exploring_included_data.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Package suggested but not available for checking: ‘refund’
Packages required but not available: ‘dplyr’ ‘FactoMineR’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘Hmisc’

Packages suggested but not available for checking: ‘dggrids’ ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Packages suggested but not available for checking:
  ‘car’ ‘Hmisc’ ‘klaR’ ‘pROC’ ‘rrlda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘RTCGA.rnaseq’ ‘ggplot2’ ‘tibble’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Packages required but not available: ‘forecast’ ‘rainbow’

Packages suggested but not available for checking: ‘fds’ ‘meboot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘afex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘rplos’ ‘rcrossref’ ‘microdemic’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘bold’ ‘BioSeqClass’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘tidyverse’ ‘sjmisc’
Error in re-building vignettes:
  ...
Quitting from lines 39-44 (Furniture.Rmd) 
Error: processing vignette ‘Furniture.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
      user system elapsed
fpca 5.858  0.039   7.565
Error in re-building vignettes:
  ...
Quitting from lines 64-76 (subgroup_fusion.Rmd) 
Error: processing vignette ‘subgroup_fusion.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘ggthemes’ ‘leaflet’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘purrr’

Packages suggested but not available for checking: ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘robustHD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘GAparsimony-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ga_parsimony
> ### Title: GA-PARSIMONY
> ### Aliases: ga_parsimony show,ga_parsimony-method
> ###   print,ga_parsimony-method print,ga_parsimony-method numericOrNA
> ### Keywords: optimize
> 
> ### ** Examples
> 
> 
> #################################
> ### Example 1: Classification ###
> #################################
> 
> # This a toy example that shows how to search, for the *iris* database, 
> # a parsimony classification NNET model with 'GAparsimony' 
> # and 'caret' packages. Validation errors and iterations have been
> # reduced to speedup the process
> 
> library(GAparsimony)
> # Training and testing Datasets
> library(caret)
Error in library(caret) : there is no package called ‘caret’
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘haplo.stats’ ‘rms’
Packages required but not available: ‘dplyr’ ‘tibble’ ‘ggplot2’ ‘rstan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘paleofire’
Running examples in ‘GDAdata-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Decathlon
> ### Title: Top performances in the Decathlon from 1985 to 2006.
> ### Aliases: Decathlon
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Decathlon, package="GDAdata")
> summary(Decathlon[, grep("P.*", names(Decathlon))])
   Polevault         P100m             Plj              Psp       
 Min.   :2.850   Min.   : 597.0   Min.   : 569.0   Min.   :418.0  
 1st Qu.:4.200   1st Qu.: 765.0   1st Qu.: 757.0   1st Qu.:622.0  
 Median :4.400   Median : 806.0   Median : 804.0   Median :672.0  
 Mean   :4.405   Mean   : 806.6   Mean   : 807.4   Mean   :674.6  
 3rd Qu.:4.650   3rd Qu.: 847.0   3rd Qu.: 857.0   3rd Qu.:726.0  
 Max.   :5.760   Max.   :1042.0   Max.   :1089.0   Max.   :941.0  
      Phj           P400m         P110h             Ppv              Pdt       
 Min.   : 396   Min.   :532   Min.   : 526.0   Min.   : 321.0   Min.   :231.0  
 1st Qu.: 696   1st Qu.:746   1st Qu.: 777.0   1st Qu.: 673.0   1st Qu.:600.0  
 Median : 749   Median :789   Median : 824.0   Median : 731.0   Median :655.0  
 Mean   : 749   Mean   :788   Mean   : 821.6   Mean   : 734.4   Mean   :657.8  
 3rd Qu.: 803   3rd Qu.:832   3rd Qu.: 868.0   3rd Qu.: 804.0   3rd Qu.:713.0  
 Max.   :1061   Max.   :998   Max.   :1044.0   Max.   :1152.0   Max.   :970.0  
      Pjt             P1500      
 Min.   : 330.0   Min.   :121.0  
 1st Qu.: 588.0   1st Qu.:607.0  
 Median : 644.0   Median :669.0  
 Mean   : 648.1   Mean   :661.7  
 3rd Qu.: 707.0   3rd Qu.:725.0  
 Max.   :1040.0   Max.   :946.0  
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘FactoMineR’

Package suggested but not available for checking: ‘WeightedCluster’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘tibble’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘AER’ ‘ivpack’
Packages suggested but not available for checking:
  ‘qvalue’ ‘haplo.stats’ ‘PredictABEL’ ‘VariABEL’
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘ggnetwork’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘NMF’ ‘pca3d’

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘genderdata’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘meboot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘DataVisualizations’ ‘DatabionicSwarm’ ‘rgl’
  ‘ProjectionBasedClustering’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spatialEco’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘leaflet’ ‘DT’ ‘purrr’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘forcats’
  ‘readr’ ‘rio’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mvmesh’ ‘SphericalCubature’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘reldist’
Package required but not available: ‘readr’

Packages suggested but not available for checking: ‘gistr’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘geojson-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: feature
> ### Title: feature class
> ### Aliases: feature
> 
> ### ** Examples
> 
> # point -> feature
> x <- '{ "type": "Point", "coordinates": [100.0, 0.0] }'
> point(x) %>% feature()
<Feature> 
  type:  Point 
  coordinates:  [100,0] 
> 
> # multipoint -> feature
> x <- '{"type": "MultiPoint", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> multipoint(x) %>% feature()
<Feature> 
  type:  MultiPoint 
  coordinates:  [[100,0],[101,1]] 
> 
> # linestring -> feature
> x <- '{ "type": "LineString", "coordinates": [ [100.0, 0.0], [101.0, 1.0] ] }'
> linestring(x) %>% feature()
<Feature> 
  type:  LineString 
  coordinates:  [[100,0],[101,1]] 
> 
> # multilinestring -> feature
> x <- '{ "type": "MultiLineString",
+  "coordinates": [ [ [100.0, 0.0], [101.0, 1.0] ], [ [102.0, 2.0], [103.0, 3.0] ] ] }'
> multilinestring(x) %>% feature()
<Feature> 
  type:  MultiLineString 
  coordinates:  [[[100,0],[101,1]],[[102,2],[103,3]]] 
> 
> # add to a data.frame
> library('tibble')
Error in library("tibble") : there is no package called ‘tibble’
Execution halted
Running ‘test-all.R’ [3s/5s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > library("geojson")
  
  Attaching package: 'geojson'
  
  The following object is masked from 'package:graphics':
  
      polygon
  
  > test_check("geojson")
  ── 1. Error: tibbles work with multipolygon inputs (@test-tibbles.R#13)  ───────
  there is no package called 'tibble'
  1: tibble::data_frame at testthat/test-tibbles.R:13
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 259 SKIPPED: 0 FAILED: 1
  1. Error: tibbles work with multipolygon inputs (@test-tibbles.R#13) 
  
  Error: testthat unit tests failed
  In addition: Warning messages:
  1: In lapply(args, enquote) :
    closing unused connection 4 (/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geojson/examples/linestring_one.geojson)
  2: In lapply(args, enquote) :
    closing unused connection 3 (/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/geojson/examples/linestring_one.geojson)
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'geojson'

The following object is masked from 'package:graphics':

    polygon

Quitting from lines 147-149 (geojson-operations.Rmd) 
Error: processing vignette ‘geojson-operations.Rmd’ failed with diagnostics:
there is no package called 'tibble'
Execution halted
Packages suggested but not available for checking:
  ‘ggmap’ ‘dplyr’ ‘ggplot2’
Error in re-building vignettes:
  ...
rgdal: version: 1.2-20, (SVN revision 725)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.0.1, April 1st, 2018, [PJ_VERSION: 501]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-7 
Loading required package: raster

Attaching package: 'raster'

The following object is masked _by_ '.GlobalEnv':

    values<-

The following objects are masked from 'package:geoknife':

    geom, values, values<-

Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Quitting from lines 66-83 (plot_geotiff.Rmd) 
Error: processing vignette ‘plot_geotiff.Rmd’ failed with diagnostics:
there is no package called 'ggmap'
Execution halted
Packages required but not available: ‘inlmisc’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘readr’ ‘plotly’

Packages suggested but not available for checking: ‘ggrepel’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘leaflet’ ‘rbokeh’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘slackr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘agricolae’ ‘DT’ ‘dplyr’ ‘tibble’ ‘ggplot2’ ‘readxl’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘readr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readr’ ‘dplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘dplyr’ ‘tidyr’ ‘purrr’ ‘ggplot2’ ‘plotly’ ‘ggthemes’
  ‘viridis’

Packages suggested but not available for checking:
  ‘vdiffr’ ‘pkgnet’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readxl’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘scatterpie’ ‘ggplot2’ ‘ggrepel’ ‘googlesheets’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘babynames’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘broom’ ‘crosstalk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tibble’ ‘plotly’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggraph’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘forcats’ ‘ggrepel’
  ‘ggforce’ ‘tidygraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmcmc’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggforce’ ‘GGEBiplotGUI’ ‘gge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘sjlabelled’ ‘sjmisc’ ‘sjstats’ ‘tibble’
  ‘tidyr’ ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘tibble’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘zeitgebr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colourpicker’ ‘ggplot2’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘rstan’

Packages suggested but not available for checking: ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘mosaicCore’ ‘tibble’

Packages suggested but not available for checking:
  ‘mosaic’ ‘dplyr’ ‘mosaicModel’ ‘broom’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘forecast’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘ggrepel’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggplotify’ ‘tibble’

Package suggested but not available for checking: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggiraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggridges’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘GGally’

Packages suggested but not available for checking: ‘rstan’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘productplots’ ‘plotly’ ‘dplyr’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘ggplot2’ ‘dplyr’ ‘tibble’ ‘ggthemes’ ‘editData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘plotly’ ‘ggplot2’ ‘readr’ ‘haven’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘cowplot’ ‘ggimage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tibble’ ‘dplyr’ ‘broom’

Package suggested but not available for checking: ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggrepel’ ‘ggsci’ ‘tidyr’ ‘purrr’ ‘dplyr’ ‘cowplot’
  ‘ggsignif’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘colourpicker’ ‘dplyr’ ‘DT’ ‘ggplot2’ ‘ggrepel’ ‘Hmisc’ ‘plotly’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking: ‘rmdformats’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘ggforce’ ‘ggrepel’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggthemes’ ‘colourpicker’ ‘dplyr’ ‘DT’ ‘GGally’ ‘tibble’

Package suggested but not available for checking: ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘forcats’ ‘vdiffr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘ggmap’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘photobiology’ ‘photobiologyWavebands’ ‘ggplot2’ ‘ggrepel’ ‘dplyr’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘purrr’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘cowplot’ ‘dplyr’ ‘ggcorrplot’ ‘ggExtra’ ‘ggplot2’ ‘ggrepel’
  ‘jmv’ ‘purrr’ ‘sjstats’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: coda
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2018 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##
Quitting from lines 18-24 (mcmc.rmd) 
Error: processing vignette ‘mcmc.rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘fxregime’
Unavailable namespace imported from by a ':::' call: ‘fxregime’
  See the note in ?`:::` about the use of this operator.
Packages suggested but not available for checking: ‘forcats’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 117-117 (GMCM-JStatSoft.Rnw) 
Error: processing vignette ‘GMCM-JStatSoft.Rnw’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘Deducer’
Package suggested but not available for checking: ‘mediation’
Error in re-building vignettes:
  ...
Loading required package: sandwich
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation
Warning in nlminb(P$t0, .obj1, x = x, w = w, ...) :
  NA/NaN function evaluation

Error: processing vignette ‘gmm_with_R.rnw’ failed with diagnostics:
 chunk 14 
Error in library(car) : there is no package called ‘car’
Execution halted
Packages suggested but not available for checking: ‘AER’ ‘car’
Running examples in ‘gmnl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AIC.gmnl
> ### Title: Akaike's Information Criterion
> ### Aliases: AIC.gmnl BIC.gmnl
> 
> ### ** Examples
> 
> 
> ## Estimate MNL model
> data("TravelMode", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Package required but not available: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘WGCNA’

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: GoodmanKruskal
Loading required package: MASS
Loading required package: car
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'car'
Quitting from lines 148-151 (GoodmanKruskal.Rmd) 
Error: processing vignette ‘GoodmanKruskal.Rmd’ failed with diagnostics:
object ‘Greene’ not found
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘cellranger’ ‘dplyr’ ‘purrr’ ‘readr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘wbstats’
Packages required but not available: ‘ggplot2’ ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GPareto’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘rglwidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘hexSticker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘sparklyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘qgraph’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘rtweet’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Packages suggested but not available for checking:
  ‘dplyr’ ‘dtplyr’ ‘ggplot2’ ‘ggrepel’ ‘taxstats’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/gRbase.Rcheck/00install.out’ for details.
Packages required but not available: ‘Gmisc’ ‘Hmisc’ ‘rms’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘rms’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tensorflow’

Packages suggested but not available for checking: ‘DiagrammeR’ ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘smooth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘inlmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘egg’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 24-33 (arrangeGrob.rmd) 
Error: processing vignette ‘arrangeGrob.rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘broom’ ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 310-321 (Growthcurver-vignette.Rmd) 
Error: processing vignette ‘Growthcurver-vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking: ‘dplyr’ ‘gsDesign’
Error in re-building vignettes:
  ...
Quitting from lines 261-285 (Introduction_gscounts.Rmd) 
Error: processing vignette ‘Introduction_gscounts.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cellWise’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘aqp’ ‘plotKML’

Packages suggested but not available for checking: ‘Hmisc’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 64-75 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggthemes’ ‘plotKML’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘purrr’

Packages suggested but not available for checking:
  ‘tidytext’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘eda4treeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mvoutlier’
Running examples in ‘h2o-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aaa
> ### Title: Starting H2O For examples
> ### Aliases: aaa
> 
> ### ** Examples
> 
> if(Sys.info()['sysname'] == "Darwin" && Sys.info()['release'] == '13.4.0'){
+  quit(save="no")
+ }else{
+  h2o.init(nthreads = 2)
+ }

H2O is not running yet, starting it now...

Note:  In case of errors look at the following log files:
    /home/hornik/tmp/scratch/RtmpSmmqKw/h2o_UnknownUser_started_from_r.out
    /home/hornik/tmp/scratch/RtmpSmmqKw/h2o_UnknownUser_started_from_r.err

openjdk version "10.0.1" 2018-04-17
OpenJDK Runtime Environment (build 10.0.1+10-Debian-4)
OpenJDK 64-Bit Server VM (build 10.0.1+10-Debian-4, mixed mode)

Starting H2O JVM and connecting: ............................................................ 
[1] "localhost"
[1] 54321
[1] TRUE
[1] -1
[1] "Failed to connect to localhost port 54321: Connection refused"
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed to connect to localhost port 54321: Connection refused
[1] 7
Error in h2o.init(nthreads = 2) : 
  H2O failed to start, stopping execution.
Execution halted
Packages suggested but not available for checking: ‘nbpMatching’ ‘lmerTest’
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘mnis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggtree’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forcats’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 34-37 (hazus_demo.Rmd) 
Error: processing vignette ‘hazus_demo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘klaR’
Package suggested but not available for checking: ‘nycflights13’
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-2>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-3>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <unnamed-chunk-4>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 86-92 (hdf5r.Rmd) 
Error: processing vignette ‘hdf5r.Rmd’ failed with diagnostics:
there is no package called 'nycflights13'
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rms’ ‘ggplot2’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘caret’ ‘cowplot’ ‘dbplyr’ ‘dplyr’ ‘ggplot2’ ‘purrr’
  ‘recipes’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘plotly’ ‘viridis’ ‘ggplot2’ ‘dendextend’ ‘seriation’

Package suggested but not available for checking: ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tibble’

Packages suggested but not available for checking: ‘Hmisc’ ‘readxl’ ‘rgho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nhanesA’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘precrec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking:
  ‘rgl’ ‘candisc’ ‘corrgram’ ‘mvinfluence’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘synbreed’
Packages required but not available: ‘cplm’ ‘DESeq2’

Package suggested but not available for checking: ‘glmmADMB’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘hesim-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: icea
> ### Title: Individualized cost-effectiveness analysis
> ### Aliases: icea icea_pw
> 
> ### ** Examples
> 
> # simulation output
> nsims <- 100
> sim <- data.frame(sim = rep(seq(nsims), 4),
+                c = c(rlnorm(nsims, 5, .1), rlnorm(nsims, 5, .1),
+                       rlnorm(nsims, 11, .1), rlnorm(nsims, 11, .1)),
+                e = c(rnorm(nsims, 8, .2), rnorm(nsims, 8.5, .1),
+                      rnorm(nsims, 11, .6), rnorm(nsims, 11.5, .6)),
+                strategy = rep(paste0("Strategy ", seq(1, 2)),
+                              each = nsims * 2),
+                grp = rep(rep(c("Group 1", "Group 2"),
+                              each = nsims), 2)
+ )
> 
> # icea
> icea.dt <- icea(sim, k = seq(0, 200000, 500), sim = "sim", strategy = "strategy",
+  grp = "grp", e = "e", c = "c")
> names(icea.dt)
[1] "summary" "mce"     "evpi"    "nmb"    
> # the probability that each strategy is the most cost-effective 
> # in each group with a willingness to pay of 20,000
> library("data.table")
> icea.dt$mce[k == 20000]
       k   strategy     grp prob
1: 20000 Strategy 1 Group 1 0.57
2: 20000 Strategy 2 Group 1 0.43
3: 20000 Strategy 1 Group 2 0.47
4: 20000 Strategy 2 Group 2 0.53
> 
> # icea_pw
> icea.pw.dt <-  icea_pw(sim,  k = seq(0, 200000, 500), comparator = "Strategy 1",
+                       sim = "sim", strategy = "strategy", e = "e", c = "c")
> names(icea.pw.dt)
[1] "summary" "delta"   "ceac"    "inmb"   
> # cost-effectiveness acceptability curve
> library("ggplot2")
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-170 (cea-vignette.Rmd) 
Error: processing vignette ‘cea-vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggimage’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking:
  ‘car’ ‘Rcmdr’ ‘RcmdrPlugin.HH’ ‘microplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggdendro’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adegenet’

Package suggested but not available for checking: ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘purrr’ ‘dplyr’ ‘tibble’ ‘broom’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘highlightHTML-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: table_id_inject
> ### Title: Table hash addition for markup
> ### Aliases: table_id_inject
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(highlightHTML)
  > 
  > test_check("highlightHTML")
  ── 1. Error: add in tags to table (@test_table_id.r#4)  ────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test_table_id.r:4
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: add in tags to table (@test_table_id.r#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 118-131 (the_basics.Rmd) 
Error: processing vignette ‘the_basics.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘rms’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘car’ ‘heplots’
Running examples in ‘HistData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Bowley
> ### Title: Bowley's data on values of British and Irish trade, 1855-1899
> ### Aliases: Bowley
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(Bowley)
> 
> # plot the data 
> with(Bowley,plot(Year, Value, type='b', 
+ 	ylab="Value of British and Irish Exports",
+ 	main="Bowley's example of the method of smoothing curves"))
> 
> # find moving averages-- use center alignment (requires width=ODD)
> require(gtools, warn.conflicts=FALSE)
Loading required package: gtools
> mav3<-running(Bowley$Value, width=3, align="center")
> mav5<-running(Bowley$Value, width=5, align="center")
> mav9<-running(Bowley$Value, width=9, align="center")
> lines(Bowley$Year[2:44], mav3, col='blue', lty=2)
> lines(Bowley$Year[3:43], mav5, col='green3', lty=3)
> lines(Bowley$Year[5:41], mav9, col='brown', lty=4)
> 
> # add lowess smooth
> lines(lowess(Bowley), col='red', lwd=2)
> 
> require(ggplot2, warn.conflicts=FALSE)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> qplot(Year,Value, data=Bowley)+geom_smooth()
Error in qplot(Year, Value, data = Bowley) : 
  could not find function "qplot"
Execution halted
Packages required but not available: ‘FactoMineR’ ‘ggplot2’ ‘ggridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘trackr’
Packages required but not available: ‘rgl’ ‘tkrgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking: ‘rms’ ‘tables’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘HMP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NMF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘horseshoe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: HS.normal.means
> ### Title: The horseshoe prior for the sparse normal means problem
> ### Aliases: HS.normal.means
> 
> ### ** Examples
> 
> #Empirical Bayes example with 20 signals, rest is noise
> #Posterior mean for the signals is plotted
> #And variable selection is performed using the credible intervals
> #And the credible intervals are plotted
> truth <- c(rep(0, 80), rep(8, 20))
> data <-  truth + rnorm(100, 1)
> tau.hat <- HS.MMLE(data, Sigma2 = 1)
> res.HS1 <- HS.normal.means(data, method.tau = "fixed", tau = tau.hat,
+ method.sigma = "fixed", Sigma2 = 1)
[1] 1000
[1] 2000
[1] 3000
[1] 4000
[1] 5000
[1] 6000
> #Plot the posterior mean against the data (signals in blue)
> plot(data, res.HS1$BetaHat, col = c(rep("black", 80), rep("blue", 20)))
> #Find the selected betas (ideally, the last 20 are equal to 1)
> HS.var.select(res.HS1, data, method = "intervals")
  [1] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0
 [75] 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1
> #Plot the credible intervals
> library(Hmisc)
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mice
Loading required package: lattice
Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  52 observations with no observed data.  These observations were removed

Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  45 of 4661 imputations with # donors < 5, consider increasing sdCutoff or using method='p.draw'


Error: processing vignette ‘Using_Hot_Deck_Data.Rnw’ failed with diagnostics:
 chunk 7 (label = zel) 
Error in library(Zelig) : there is no package called 'Zelig'
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘data.tree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘caret’

Packages suggested but not available for checking: ‘rgl’ ‘hyperSpec’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘Hmisc’ ‘tibble’ ‘tidyr’ ‘dplyr’
Running ‘testInteractive.R’ [1s/1s]
  Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library('testthat')
  > 
  > test_check('htmlTable')
  Loading required package: htmlTable
  ── 1. Error: HTML code is properly escaped (@test-htmlTable.R#398)  ────────────
  there is no package called 'tibble'
  1: tibble::as.tibble at testthat/test-htmlTable.R:398
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 447 SKIPPED: 1 FAILED: 1
  1. Error: HTML code is properly escaped (@test-htmlTable.R#398) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 101-141 (tables.Rmd) 
Error: processing vignette ‘tables.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘tidyr’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
No encoding supplied: defaulting to UTF-8.
Quitting from lines 47-50 (htmltab.Rmd) 
Error: processing vignette ‘htmltab.Rmd’ failed with diagnostics:
there is no package called 'tidyr'
Execution halted
Package suggested but not available for checking: ‘HTSFilter’
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘DESeq2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘GGally’ ‘EnvStats’ ‘viridis’
Package suggested but not available for checking: ‘purrr’
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggmap’ ‘ggplot2’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘hurricaneexposuredata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘nycflights13’ ‘ggplot2’
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking: ‘broom’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘adegenet’
Running examples in ‘HWxtest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hwx.test
> ### Title: Test for HW by either full enumeration or Monte Carlo.
> ### Aliases: hwx.test
> 
> ### ** Examples
> 
> # Data from Louis and Dempster 1987 Table 2 and Guo and Thompson 1992 Figure 2:
> c <- c(0,3,1,5,18,1,3,7,5,2)
> hwx.test(c)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
> # To see a histogram of the LLR statistic:
> hwx.test(c, histobins=TRUE)

*****    Sample of 45 diploids with 4 alleles
Full enumeration of 162365 tables to test for HW

P value (LLR)   = 0.012945
P value (Prob)  = 0.017442
P value (U)     = 0.003343 (test for heterozygote excess)
P value (Chisq) = 0.020170
Loading required namespace: ggplot2
Failed with error:  ‘there is no package called ‘ggplot2’’
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 6-18 (HWxtest.Rmd) 
Error: processing vignette ‘HWxtest.Rmd’ failed with diagnostics:
there is no package called 'adegenet'
Execution halted
Package required but not available: ‘InformationValue’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DiagrammeR’ ‘dplyr’ ‘pixiedust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’

Packages suggested but not available for checking:
  ‘dataRetrieval’ ‘ggplot2’ ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘SWAT2R’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘readr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘hydrostats-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flood.length.max
> ### Title: Calculates the maximum flood length in a time series.
> ### Aliases: flood.length.max
> 
> ### ** Examples
> 
> 
> data(Cooper)
> Cooper<-ts.format(Cooper)
> 
> flood.length.max(Cooper, threshold = 50000, ind.days = 5)
  max.duration
1           40
> 
> # Return annual maximum flood length based on calendar year using ddply (from plyr package) 
> require(plyr)
Loading required package: plyr
> Cooper$Year=format(Cooper$Date, format="%Y")
> ddply(Cooper, .(Year), flood.length.max, threshold = 50000)
   Year max.duration
1  1967            0
2  1968           13
3  1969            0
4  1970            0
5  1971           10
6  1972            6
7  1973           17
8  1974           40
9  1975            2
10 1976           21
11 1977           19
12 1978            0
13 1979            8
14 1980            1
15 1981            3
16 1982            0
17 1983           10
18 1984            0
19 1985            0
20 1986            7
21 1987            0
> 
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dplyr’
> Cooper %>%
+ dplyr::group_by(Year) %>%
+ dplyr::do(flood.length.max(., threshold = 50000))
Error in Cooper %>% dplyr::group_by(Year) %>% dplyr::do(flood.length.max(.,  : 
  could not find function "%>%"
Execution halted
Package required but not available: ‘unbalanced’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘data.tree’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IalsaSynthesis)
  > 
  > test_check("IalsaSynthesis")
  ── 1. Error: (unknown) (@test-extract.R#8)  ────────────────────────────────────
  there is no package called 'readr'
  1: readr::read_file at testthat/test-extract.R:8
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-extract.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘dplyr’ ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘ibhm.tests.R’ [3s/4s]
Running the tests in ‘tests/ibhm.tests.R’ failed.
Complete output:
  > library(IBHM)
  Loading required package: compiler
  Loading required package: DEoptim
  Loading required package: parallel
  
  DEoptim package
  Differential Evolution algorithm in R
  Authors: D. Ardia, K. Mullen, B. Peterson and J. Ulrich
  
  Loading required package: cmaes
  Loading required package: Rcpp
  > source('utils.R')
  > 
  > 
  > (test.Tanh <- function(){
  +   x <- seq(-6,6,length.out=400)
  +   y <- tanh(x)
  +   
  +   set.seed(123)  
  +   m <- TrainIBHM(x,y, ConfigureIBHM(scal.candidates='dot.pr', activ.candidates='tanh'))  
  +   stopifnot(summary(m)$rmse<0.1) 
  +   cat('tanh - ok\n')
  + })()
  Error in summary(m)$rmse < 0.1 : $ operator is invalid for atomic vectors
  Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Package suggested but not available for checking: ‘dynsurv’
Packages required but not available:
  ‘car’ ‘coefplot’ ‘forecast’ ‘openair’ ‘papeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘tidyr’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘rstan’ ‘dplyr’ ‘tidyr’ ‘bayesplot’ ‘ggplot2’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘DendSer’
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘FRK’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggrepel’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readxl’ ‘qdap’

Packages suggested but not available for checking: ‘ie2miscdata’ ‘iemisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘iemisc’ ‘ie2misc’ ‘ie2miscdata’ ‘qdap’
Packages required but not available: ‘listless’ ‘IAPWS95’

Packages suggested but not available for checking: ‘ie2misc’ ‘optiRum’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘NSM3’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘filesstrings’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘demography’ ‘rainbow’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dae’ ‘ggplot2’ ‘Hmisc’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mediation’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘caret’ ‘lime’ ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’ ‘tidyselect’

Packages suggested but not available for checking: ‘Lahman’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘importar-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: import
> ### Title: This function imports/loads packages as in 'Python', i.e.,
> ###   "import package as alias"
> ### Aliases: import
> 
> ### ** Examples
> 
> import(dplyr, d)
Error in library(package., character.only = TRUE) : 
  there is no package called ‘dplyr’
Calls: import -> <Anonymous> -> withCallingHandlers -> library
Execution halted
Packages required but not available: ‘Hmisc’ ‘haven’

Package suggested but not available for checking: ‘compareGroups’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘PSF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forecast’ ‘ggplot2’ ‘imputeTS’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘rccmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘cowplot’ ‘dplyr’ ‘drc’ ‘DT’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘iNEXT’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘ggplot2’

Packages suggested but not available for checking: ‘broom’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘descriptr’ ‘haven’ ‘readr’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘minfi’
Package suggested but not available for checking: ‘dbplyr’
Error in re-building vignettes:
  ...
Quitting from lines 157-158 (getting_started.Rmd) 
Error: processing vignette ‘getting_started.Rmd’ failed with diagnostics:
there is no package called 'dbplyr'
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘ggmap’ ‘rgl’ ‘sphereplot’ ‘dplyr’ ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘missMDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘spcosa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘FactoMineR’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 16-23 (interlineaR.Rmd) 
Error: processing vignette ‘interlineaR.Rmd’ failed with diagnostics:
there is no package called 'kableExtra'
Execution halted
Packages required but not available: ‘ggplot2’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘dplyr’ ‘eurostat’ ‘tidyr’ ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘haven’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘DT’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Fgmutils’ ‘rbokeh’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘cowplot’ ‘ggplot2’ ‘GGally’ ‘xergm’ ‘comtradr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘NMF’
Error in re-building vignettes:
  ...
Quitting from lines 45-47 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'NMF'
Execution halted
Running examples in ‘janeaustenr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: austen_books
> ### Title: Tidy data frame of Jane Austen's 6 completed, published novels
> ### Aliases: austen_books
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(janeaustenr)
  > 
  > test_check("janeaustenr")
  ── 1. Error: (unknown) (@test_austen_books.R#5)  ───────────────────────────────
  there is no package called 'dplyr'
  1: suppressPackageStartupMessages(library(dplyr)) at testthat/test_austen_books.R:5
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(dplyr)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_austen_books.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘iClick’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘car’ ‘ggplot2’ ‘emmeans’ ‘GGally’ ‘afex’ ‘ggridges’

Package suggested but not available for checking: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘BaBooN’ ‘mitml’
Packages required but not available:
  ‘dplyr’ ‘leaflet’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘jpmesh’ ‘dplyr’ ‘leaflet’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘broom’ ‘brms’ ‘cowplot’ ‘ggstance’ ‘huxtable’ ‘rstanarm’ ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘cowplot’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘clustMD’ ‘ggplot2’ ‘Hmisc’
Packages required but not available:
  ‘MVN’ ‘forecast’ ‘nonlinearTseries’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘tidytext’
Error in re-building vignettes:
  ...
Quitting from lines 13-26 (methods.Rmd) 
Error: processing vignette ‘methods.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘keras’ ‘dplyr’

Packages suggested but not available for checking: ‘tensorflow’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tensorflow’ ‘tfruns’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: knitr
Loading required package: kfigr
knitr hook "anchor" is now available
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 26-28 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
could not find function "qplot"
Execution halted
Package required but not available: ‘questionr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘longitudinalData’ ‘kml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘longitudinalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘longitudinalData’ ‘kml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 17-32 (cars.Rmd) 
Error: processing vignette ‘cars.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(knitrProgressBar)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(withr)
  > 
  > test_check("knitrProgressBar")
  Read 7 items
  Read 7 items
  ── 1. Error: regular progress works (@test-kpb.R#14)  ──────────────────────────
  there is no package called 'purrr'
  1: with_mock(is_interactive = function() TRUE, is_in_knitr = function() FALSE, {
         pb <- progress_estimated(5)
         withr::with_output_sink("test_pb.txt", run_pb())
         expect_match(scan("test_pb.txt", what = character(), quiet = TRUE), "|========================================================================================================|100% ~0 s remaining")
         file.remove("test_pb.txt")
     }) at testthat/test-kpb.R:14
  2: with_mock_(.dots = .dots, .parent = .parent, .env = .env)
  3: evaluate_with_mock_env(get_code_dots(dots), mock_env, .parent)
  4: lazyeval::lazy_eval(code[[length(code)]])
  5: eval(x$expr, x$env, emptyenv())
  6: eval(x$expr, x$env, emptyenv())
  7: withr::with_output_sink("test_pb.txt", run_pb()) at testthat/test-kpb.R:20
  8: force(code)
  9: run_pb()
  10: purrr::map at testthat/test-kpb.R:6
  11: getExportedValue(pkg, name)
  12: asNamespace(ns)
  13: getNamespace(ns)
  14: tryCatch(loadNamespace(name), error = function(e) stop(e))
  15: tryCatchList(expr, classes, parentenv, handlers)
  16: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  17: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 16 SKIPPED: 0 FAILED: 1
  1. Error: regular progress works (@test-kpb.R#14) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In .Internal(get(x, envir, mode, inherits)) :
    closing unused connection 4 (kpb_output.log)
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 131-134 (example_progress_bars.Rmd) 
Error: processing vignette ‘example_progress_bars.Rmd’ failed with diagnostics:
there is no package called 'purrr'
Execution halted
Packages suggested but not available for checking: ‘rgl’ ‘tibble’
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘KODAMA-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dinisurface
> ### Title: Ulisse Dini Data Set Generator
> ### Aliases: dinisurface
> ### Keywords: dataset
> 
> ### ** Examples
> 
> require("rgl")
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
> x=dinisurface()
> open3d()
Error in open3d() : could not find function "open3d"
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘plotly’
Error in re-building vignettes:
  ...
Quitting from lines 24-28 (copper_mining_2d.Rmd) 
Error: processing vignette ‘copper_mining_2d.Rmd’ failed with diagnostics:
there is no package called 'plotly'
Execution halted
Package suggested but not available for checking: ‘FactoClass’
Packages suggested but not available for checking: ‘OceanView’ ‘rgl’
Running examples in ‘ks-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.kdde
> ### Title: Plot for kernel density derivative estimate
> ### Aliases: plot.kdde
> ### Keywords: hplot
> 
> ### ** Examples
> 
> ## univariate example
> data(tempb)
> fhat1 <- kdde(x=tempb[,"tmin"], deriv.order=1)   ## gradient [df/dx, df/dy]
> plot(fhat1, xlab="Min. temp.")                   ## df/dx
> points(20,predict(fhat1, x=20))
> 
> ## bivariate example
> fhat1 <- kdde(x=tempb[,c("tmin", "tmax")], deriv.order=1)
> plot(fhat1, display="quiver")
Error: Install the OceanView package as it is required.
Execution halted
Package suggested but not available for checking: ‘rockchalk’
Package required but not available: ‘haven’

Packages suggested but not available for checking: ‘dplyr’ ‘questionr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 124-133 (labelVector.Rmd) 
Error: processing vignette ‘labelVector.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package suggested but not available for checking: ‘crs’
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘GGally’ ‘ggplot2’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rms’ ‘Hmisc’ ‘lmerTest’
Package required but not available: ‘styler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggforce’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘treemap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘heplots’
Error in re-building vignettes:
  ...
Quitting from lines 55-71 (using-latex2exp.Rmd) 
Error: processing vignette ‘using-latex2exp.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘lmerTest’ ‘riskRegression’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘leaflet’

Package which this enhances but not available for checking: ‘geojsonio’
Running examples in ‘lawn-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: lawn_unkinkpolygon
> ### Title: Unkink polygon
> ### Aliases: lawn_unkinkpolygon
> 
> ### ** Examples
> 
> x <- '{
+   "type": "Feature",
+   "properties": {},
+   "geometry": {
+     "type": "Polygon",
+       "coordinates": [[[0, 0], [2, 0], [0, 2], [2, 2], [0, 0]]]
+    }
+ }'
> lawn_unkinkpolygon(x)
<FeatureCollection>
  Bounding box: 0.0 0.0 2.0 2.0
  No. features: 2
  No. points: 16
  Properties: NULL
> view(x)
Error: Please install leaflet
Execution halted
Package required but not available: ‘weights’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ldat.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘gistr’
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: survival
Loading required package: Matrix
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘addTracks.Rnw’ failed with diagnostics:
 chunk 14 (label = addQplot) 
Error in ggplotGrob({ : could not find function "ggplotGrob"
Execution halted
Packages required but not available: ‘ecd’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘leaflet’ ‘leaflet.extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘leaflet’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘crosstalk’ ‘viridis’

Package suggested but not available for checking: ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘LEAP_Vignette.Rnw’ failed with diagnostics:
 chunk 10 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pROC’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘syuzhet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  LBLasso.c:98:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBlogistic.c:100:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  LBmultilogistic.c:110:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ggm.c:69:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ising.c:83:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  potts.c:99:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Libra.Rcheck/00install.out’ for details.
Packages required but not available: ‘mapview’ ‘mapedit’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘demography’ ‘forecast’
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/lifecontingencies.Rcheck/vign_test/lifecontingencies") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/pensionfunding.Rmd’
(Is a VignetteBuilder field missing?)
Package:  lifecontingencies
Authors:  Giorgio Alfredo Spedicato [cre,aut], Reinhold Kainhofer [ctb], Kevin J.
    Owens [ctb], Christophe Dutang [ctb], Ernesto Schirmacher[ctb], Gian Paolo Clemente [ctb]
Version:  1.3.2
Date:     2017-12-09
BugReport: http://github.com/spedygiorgio/lifecontingencies/issues

Loading required package: markovchain
Package:  markovchain
Version:  0.6.9.8-1
Date:     2017-08-15
BugReport: http://github.com/spedygiorgio/markovchain/issues

Loading required package: parallel

Error: processing vignette ‘mortality_projection.Rnw’ failed with diagnostics:
 chunk 2 (label = load) 
Error in library(demography) : there is no package called 'demography'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘modelr’ ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘mlr’ ‘keras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘leaflet’ ‘leaflet.minicharts’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘mlr’
Packages suggested but not available for checking: ‘tibble’ ‘purrr’
Packages required but not available:
  ‘mlr’ ‘dplyr’ ‘breakDown’ ‘forestmodel’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mlr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘lle-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_lle
> ### Title: Plot LLE results
> ### Aliases: plot_lle
> 
> ### ** Examples
> 
> 	data( lle_scurve_data )
> 	X <- lle_scurve_data
> 	Y <- lle( X, m=2, k=12 )$Y
finding neighbours
calculating weights
computing coordinates
> 	plot_lle( Y, X, FALSE, col="red", inter=TRUE )
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
Error in plot3d(Y, col = col) : could not find function "plot3d"
Calls: plot_lle
Execution halted
Package required but not available: ‘ggtern’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: Matrix
Quitting from lines 95-111 (lmer.Rnw) 
Error: processing vignette ‘lmer.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘SPEI’
Packages suggested but not available for checking: ‘car’ ‘dynlm’ ‘AER’
Package suggested but not available for checking: ‘mosaic’
Packages required but not available: ‘rms’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 7-30 (logitnorm.Rmd) 
Error: processing vignette ‘logitnorm.Rmd’ failed with diagnostics:
could not find function "exit"
Execution halted
Packages suggested but not available for checking: ‘rgl’ ‘RDRToolbox’
Packages suggested but not available for checking:
  ‘bayesplot’ ‘rstan’ ‘rstanarm’
Running ‘testthat.R’ [4s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(loo)
  This is loo version 2.0.0.
  **NOTE: As of version 2.0.0 loo defaults to 1 core but we recommend using as many as possible. Use the 'cores' argument or set options(mc.cores = NUM_CORES) for an entire session. Visit mc-stan.org/loo/news for details on other changes.
  
  Attaching package: 'loo'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  > Sys.setenv("R_TESTS" = "")
  > test_check("loo")
  ── 1. Error: (unknown) (@test_psis.R#2)  ───────────────────────────────────────
  there is no package called 'rstanarm'
  1: suppressPackageStartupMessages(library(rstanarm)) at testthat/test_psis.R:2
  2: withCallingHandlers(expr, packageStartupMessage = function(c) invokeRestart("muffleMessage"))
  3: library(rstanarm)
  4: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 341 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_psis.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘shapes’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Hmisc’

Packages suggested but not available for checking: ‘car’ ‘mitml’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘car’ ‘mediation’ ‘glmmADMB’ ‘lmerTest’ ‘rstan’ ‘rstanarm’
Packages suggested but not available for checking: ‘ggplot2’ ‘broom’
Error in re-building vignettes:
  ...
Quitting from lines 69-75 (lspline.Rmd) 
Error: processing vignette ‘lspline.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggmcmc’ ‘ggplot2’
Error in re-building vignettes:
  ...
Loading required package: mcmc
Loading required package: MHadaptive
Loading required package: MASS
Loading required package: numDeriv
Quitting from lines 13-17 (example-plots.Rmd) 
Error: processing vignette ‘example-plots.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘broom’ ‘dplyr’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: lucid
Loading required package: lattice
Quitting from lines 190-193 (lucid_printing.Rmd) 
Error: processing vignette ‘lucid_printing.Rmd’ failed with diagnostics:
could not find function "%>%"
Execution halted
Packages suggested but not available for checking: ‘caret’ ‘Hmisc’
Running examples in ‘lulcc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: allow
> ### Title: Implement decision rules for land use change
> ### Aliases: allow
> 
> ### ** Examples
> 
> 
> ## Plum Island Ecosystems
> 
> ## load observed land use data
> obs <- ObsLulcRasterStack(x=pie,
+                    pattern="lu",
+                    categories=c(1,2,3),
+                    labels=c("forest","built","other"),
+                    t=c(0,6,14))
> 
> ## get land use values
> x <- getValues(obs[[1]])
> x <- x[!is.na(x)]
> 
> ## create vector of arbitrary land use history values
> hist <- sample(1:10, length(x), replace=TRUE)
> 
> ## calculate demand and get change direction for first timestep
> dmd <- approxExtrapDemand(obs=obs, tout=0:14)
Warning in total(x = obs) :
  missing argument 'categories': getting categories from 'x'
Error in loadNamespace(name) : there is no package called ‘Hmisc’
Calls: approxExtrapDemand ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘readxl’

Packages suggested but not available for checking:
  ‘RLumShiny’ ‘RLumModel’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘qgraph’ ‘dplyr’ ‘semPlot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘depth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking: ‘moveHMM’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘machina’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘etl’ ‘dplyr’ ‘readr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘dbplyr’ ‘broom’ ‘ggmap’ ‘leaflet’ ‘clifro’

VignetteBuilder packages required for checking but not installed:
  ‘etl’ ‘dplyr’ ‘ggplot2’ ‘leaflet’ ‘clifro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘R2wd’
Error in re-building vignettes:
  ...
Quitting from lines 33-38 (maddison_project_database.Rmd) 
Error: processing vignette ‘maddison_project_database.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘R2wd’ ‘ggplot2’
Packages required but not available:
  ‘forecast’ ‘forecastHybrid’ ‘ggplot2’ ‘tidyr’ ‘ggseas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘imager’
Packages suggested but not available for checking:
  ‘ggplot2’ ‘gapminder’ ‘tesseract’
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: device
> ### Title: Magick Graphics Device
> ### Aliases: device image_graph image_device image_draw image_capture
> 
> ### ** Examples
> 
> # Regular image
> frink <- image_read("https://jeroen.github.io/images/frink.png")
> 
> # Produce image using graphics device
> fig <- image_graph(res = 96)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = cyl)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 414-418 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘GEOquery’ ‘GEOmetadb’ ‘beadarray’ ‘lumi’ ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘haven’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘leaflet’ ‘plotly’
Packages required but not available: ‘forecast’ ‘smooth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘leaflet’ ‘leaflet.extras’ ‘mapview’

Package which this enhances but not available for checking: ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘leaflet’ ‘spocc’ ‘gistr’

Packages suggested but not available for checking: ‘ggmap’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘gapminder’

Package which this enhances but not available for checking: ‘AER’
Error in re-building vignettes:
  ...
Quitting from lines 347-355 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘biomod2’
Error in re-building vignettes:
  ...
Loading required package: lme4
Loading required package: Matrix
Loading required package: parallel
This is marked 1.2.1


Error: processing vignette ‘markedVignette.Rnw’ failed with diagnostics:
 chunk 4 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking:
  ‘broom’ ‘ggplot2’ ‘Hmisc’
Running examples in ‘MARSS-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: augment.marssMLE
> ### Title: Return the model predicted values, residuals, and optionally
> ###   confidence intervals
> ### Aliases: augment.marssMLE augment_dfa augment_marss augmentmarxss
> 
> ### ** Examples
> 
>   dat <- t(harborSeal)
>   dat <- dat[c(2,11,12),]
>   MLEobj <- MARSS(dat, model=list(Z=factor(c("WA","OR","OR"))))
Success! abstol and log-log tests passed at 37 iterations.
Alert: conv.test.slope.tol is 0.5.
Test with smaller values (<0.1) to ensure convergence.

MARSS fit is
Estimation method: kem 
Convergence test: conv.test.slope.tol = 0.5, abstol = 0.001
Estimation converged in 37 iterations. 
Log-likelihood: 13.72233 
AIC: -11.44465   AICc: -8.918339   
 
                Estimate
A.OR.SouthCoast  0.49280
R.diag           0.02509
U.WA             0.06171
U.OR             0.03686
Q.(WA,WA)        0.01082
Q.(OR,OR)        0.00439
x0.WA            7.41712
x0.OR            6.56460
Initial states (x0) defined at t=0

Standard errors have not been calculated. 
Use MARSSparamCIs to compute CIs and bias estimates.

> 
> library(broom)
Error in library(broom) : there is no package called ‘broom’
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 65-75 (././Sections/4_MonteCarloResults.Rnw) 
Quitting from lines 39-40 (././Sections/4_MonteCarloResults.Rnw) 
Error: processing vignette ‘matching.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘WhatIf’
Packages required but not available: ‘weights’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘car’

Package suggested but not available for checking: ‘rglwidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘rmapshaper’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘extracat’ ‘dplyr’ ‘seriation’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘spsurvey’
Error in re-building vignettes:
  ...
Quitting from lines 187-200 (MBHdesign.Rnw) 
Error: processing vignette ‘MBHdesign.Rnw’ failed with diagnostics:
there is no package called 'spsurvey'
Execution halted
Found the following significant warnings:
  mue_nelmC.cpp:147:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:185:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nelmC.cpp:230:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:135:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:173:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  mue_nrmC.cpp:218:22: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mcIRT.Rcheck/00install.out’ for details.
Packages required but not available: ‘rstan’ ‘overlapping’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ecr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘car’

Depends: includes the non-default packages:
  ‘lattice’ ‘locfit’ ‘maptools’ ‘quantreg’ ‘RANN’ ‘SparseM’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘McSpatial-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmmprobit 
> ### Title: GMM Spatial Probit
> ### Aliases: 'gmmprobit '
> ### Keywords: Parmametric Models Spatial AR Model Discrete Choice Models
> 
> ### ** Examples
> 
> set.seed(9947)
> cmap <- readShapePoly(system.file("maps/CookCensusTracts.shp",
+   package="McSpatial"))
Warning: use rgdal::readOGR or sf::st_read
> cmap <- cmap[cmap$CHICAGO==1&cmap$CAREA!="O'Hare",]
> lmat <- coordinates(cmap)
> dnorth <- geodistance(lmat[,1],lmat[,2], -87.627800, 
+ 	41.881998, dcoor=TRUE)$dnorth
> cmap <- cmap[dnorth>0,]
> wmat <- makew(cmap)$wmat
Loading required package: Matrix
Loading required package: spData
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`
> n = nrow(wmat)
> rho = .4
> x <- runif(n,0,10)
> ystar <- as.numeric(solve(diag(n) - rho*wmat)%*%(x + rnorm(n,0,2)))
> y <- ystar>quantile(ystar,.4)
> fit <- gmmprobit(y~x,  wmat=wmat)
Error in library(car) : there is no package called ‘car’
Calls: gmmprobit -> library
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘smacof’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘smacof’ ‘clusterSim’ ‘symbolicDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘babynames’ ‘dbplyr’ ‘dplyr’ ‘ggplot2’ ‘mosaic’ ‘tidyverse’

Packages suggested but not available for checking:
  ‘Lahman’ ‘etl’ ‘macleish’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dynlm’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 50-60 (advanced.Rmd) 
Error: processing vignette ‘advanced.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 61-67 (cost-report-analysis.Rmd) 
Error: processing vignette ‘cost-report-analysis.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘Hmisc’

Depends: includes the non-default packages:
  ‘seqinr’ ‘pcaMethods’ ‘Matrix’ ‘ROCR’ ‘Hmisc’ ‘KernSmooth’ ‘seqLogo’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘leaflet’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggthemes’ ‘tidyr’ ‘dplyr’ ‘readxl’ ‘DT’ ‘ggplot2’ ‘plotly’ ‘mem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘cowplot’ ‘ggimage’ ‘shadowtext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘purrr’ ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘adegenet’
Running examples in ‘memgene-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: codomToPropShared
> ### Title: Find proportion of shared alleles genetic distances from a
> ###   codominant alleles matrix
> ### Aliases: codomToPropShared
> 
> ### ** Examples
> 
> 
> radialData <- read.csv(system.file("extdata/radial.csv", package="memgene"))
> radialGen <- radialData[, -c(1,2)]
> radialDM <- codomToPropShared(radialGen)
Loading required package: adegenet
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘adegenet’
Error: memgene:  Please install the adegenet package to find the proportion of shared alleles
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-30 (memgeneTutorial.Rnw) 
Error: processing vignette ‘memgeneTutorial.Rnw’ failed with diagnostics:
there is no package called 'adegenet'
Execution halted
Packages which this enhances but not available for checking: ‘AER’ ‘car’
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘DT’ ‘ggplot2’ ‘broom’

Package suggested but not available for checking: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggvis’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘mixOmics’ ‘rattle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘taxa’ ‘ggplot2’ ‘taxize’ ‘traits’ ‘dplyr’ ‘readr’ ‘ggfittext’
  ‘ggrepel’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘edarf’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘preprocomb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GEOquery’ ‘GEOmetadb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘forcats’ ‘ggplot2’ ‘purrr’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘GEOquery’
Packages suggested but not available for checking: ‘GEOquery’ ‘doSMP’
Packages suggested but not available for checking: ‘HTSFilter’ ‘DESeq2’
Error in re-building vignettes:
  ...

Error: processing vignette ‘metaRNASeq.Rnw’ failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Package suggested but not available for checking: ‘semPlot’
Packages required but not available: ‘ggplot2’ ‘nullabor’ ‘dplyr’ ‘ggpubr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘metricsgraphics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mjs_add_confidence_band
> ### Title: Add a confidence band to line plot
> ### Aliases: mjs_add_confidence_band
> 
> ### ** Examples
> 
> require(binom)
Loading required package: binom
> require(dplyr)
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘dplyr’
> 
> set.seed(1492)
> binom.confint(x=sample(2:30, 100, replace=TRUE), n = 100, tol = 1e-8,
+               methods="bayes") %>%
+   mutate(x=1:100) -> bdat
Error in mutate(., x = 1:100) : could not find function "mutate"
Calls: %>% ... eval -> _fseq -> freduce -> withVisible -> <Anonymous>
Execution halted
Package required but not available: ‘revdbayes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘depth’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RTisean’ ‘tsDyn’ ‘forecast’
Error in re-building vignettes:
  ...
Quitting from lines 17-33 (Discriminability.Rmd) 
Error: processing vignette ‘Discriminability.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘grasp2db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘qdap’
Error in re-building vignettes:
  ...
Quitting from lines 95-96 (Safe-Substitution.Rmd) 
Error: processing vignette ‘Safe-Substitution.Rmd’ failed with diagnostics:
there is no package called 'qdap'
Execution halted
Package suggested but not available for checking: ‘structSSI’
Packages suggested but not available for checking:
  ‘car’ ‘haven’ ‘mitml’ ‘sjlabelled’
Running examples in ‘miceadds-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mi.anova
> ### Title: Analysis of Variance for Multiply Imputed Data Sets (Using the
> ###   D_2 Statistic)
> ### Aliases: mi.anova
> ### Keywords: ANOVA mids
> 
> ### ** Examples
> 
> #############################################################################
> # EXAMPLE 1: nhanes2 data | two-way ANOVA
> #############################################################################
> 
> library(mice)
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Packages required but not available: ‘systemfit’ ‘car’

Package suggested but not available for checking: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘systemfit’
Packages suggested but not available for checking: ‘dplyr’ ‘broom’ ‘car’
Package suggested but not available for checking: ‘VIM’
Packages required but not available: ‘GJRM’ ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MVN’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [10s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2016 Nuno Fachada
  > # Distributed under the MIT License (http://opensource.org/licenses/MIT)
  > 
  > library(testthat)
  > 
  > test_check("micompr")
  Loading required package: micompr
  ── 1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R
  subscript out of bounds
  1: assumptions(cmp) at testthat/test_cmpoutput.R:214
  2: assumptions.cmpoutput(cmp)
  
  ── 2. Error: micomp assumptions have the correct properties (@test_micomp.R#281)
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette ‘paper.Rnw’ failed with diagnostics:
subscript out of bounds
Execution halted
Packages required but not available: ‘Hmisc’ ‘HH’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘readr’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Quitting from lines 634-643 (milr-intro.Rmd) 
Error: processing vignette ‘milr-intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘testthis’
Packages required but not available: ‘ggplot2’ ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: contour3d
> ### Title: Draw an Isosurface, a Three Dimension Contour Plot
> ### Aliases: contour3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: Draw a ball
>   f <- function(x, y, z)x^2+y^2+z^2
>   x <- seq(-2,2,len=20)
>   contour3d(f,4,x,x,x)
Error in loadRGL() : rgl is mot available
Calls: contour3d -> drawScene.rgl -> loadRGL
Execution halted
Packages required but not available: ‘ggplot2’ ‘GGally’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘car’ ‘ggplot2’
Packages required but not available: ‘mixOmics’ ‘ggplot2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rgl’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
mixpack: a package for mixture components analysis
Quitting from lines 17-21 (mixture_components.Rmd) 
Error: processing vignette ‘mixture_components.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggmcmc’ ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘pitchRx’ ‘viridis’ ‘ggplot2’ ‘plotly’ ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘sparklyr’ ‘purrr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘minfi’ ‘GEOquery’
Error in re-building vignettes:
  ...
Quitting from lines 73-76 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'minfi'
Execution halted
Packages suggested but not available for checking: ‘car’ ‘AER’ ‘ggplot2’
Running examples in ‘mlogit-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hmftest
> ### Title: Hausman-McFadden Test
> ### Aliases: hmftest hmftest.formula hmftest.mlogit
> ### Keywords: htest
> 
> ### ** Examples
> 
> 
> ## from Greene's Econometric Analysis p. 731
> 
> data("TravelMode",package="AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Running ‘AER.R’ [0s/1s]
Running the tests in ‘tests/AER.R’ failed.
Complete output:
  > data("BankWages", package = "AER")
  Error in find.package(package, lib.loc, verbose = verbose) : 
    there is no package called 'AER'
  Calls: data -> find.package
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Quitting from lines 249-251 (mlogit.rnw) 
Error: processing vignette ‘mlogit.rnw’ failed with diagnostics:
there is no package called 'AER'
Execution halted
Package required but not available: ‘mlr’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mlr’ ‘smoof’

Packages suggested but not available for checking:
  ‘cmaesr’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘adabag’ ‘bartMachine’ ‘caret’ ‘clusterSim’ ‘crs’ ‘Hmisc’ ‘klaR’
  ‘mlrMBO’ ‘refund’ ‘rrlda’ ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dynsurv’ ‘AER’
Error in re-building vignettes:
  ...
Loading required package: basefun
Loading required package: variables
Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Attaching package: 'flexsurv'

The following objects are masked from 'package:eha':

    Hgompertz, Hllogis, Hlnorm, Hweibull, dgompertz, dllogis,
    hgompertz, hllogis, hlnorm, hweibull, pgompertz, pllogis,
    qgompertz, qllogis, rgompertz, rllogis


Attaching package: 'grid'

The following object is masked from 'package:variables':

    unit

Loading required package: RColorBrewer
Loading required package: mvtnorm
Loading required package: TH.data

Attaching package: 'TH.data'

The following object is masked from 'package:HSAUR3':

    birds

The following object is masked from 'package:MASS':

    geyser

trying URL ‘https://zenodo.org/record/17179/files/DVC.tgz’
Content type 'application/octet-stream' length 2292581 bytes (2.2 MB)
==================================================
downloaded 2.2 MB

Quitting from lines 1213-1219 (mlt.Rnw) 
Error: processing vignette ‘mlt.Rnw’ failed with diagnostics:
there is no package called 'AER'
Execution halted
Packages required but not available: ‘qgraph’ ‘dplyr’ ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mma’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DirichletReg’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘adegenet’ ‘pegas’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘cowplot’ ‘ggplot2’ ‘tidyr’
Error in re-building vignettes:
  ...
Quitting from lines 304-389 (modcmfitrOverview.Rmd) 
Error: processing vignette ‘modcmfitrOverview.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggbeeswarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘ggplot2’ ‘readr’

Packages suggested but not available for checking:
  ‘dbplyr’ ‘nycflights13’ ‘tidypredict’ ‘dbplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ModelGood-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: AutoSelectLRM
> ### Title: Automated backward elemination for logistic regression
> ### Aliases: AutoSelectLRM
> 
> ### ** Examples
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/ModelMetrics.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘janitor’ ‘broom’

Packages suggested but not available for checking: ‘tidyverse’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mapedit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘modmarg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: marg.ivreg
> ### Title: Predicted Margins for 'ivreg' objects from the 'AER' package
> ### Aliases: marg.ivreg
> 
> ### ** Examples
> 
> # From ?AER::ivreg
> 
> # data
> data("CigarettesSW", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Packages suggested but not available for checking: ‘smoof’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 106-114 (Basic_Usage.Rmd) 
Error: processing vignette ‘Basic_Usage.Rmd’ failed with diagnostics:
there is no package called 'smoof'
Execution halted
Package required but not available: ‘tolerance’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘alphahull’ ‘rgl’

Package suggested but not available for checking: ‘rglwidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘crawl’ ‘ggmap’ ‘ggplot2’ ‘moveHMM’ ‘car’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘geomorph’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘nycflights13’ ‘dbplyr’ ‘dplyr’
Running examples in ‘MonetDBLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: src_monetdb
> ### Title: dplyr integration from MonetDBLite
> ### Aliases: src_monetdb src_monetdblite
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Running ‘testthat.R’ [14s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > # Sys.setenv("MONETDBLITE_INMEMORY" = "yes")
  > # test_check("MonetDBLite")
  > Sys.setenv("MONETDBLITE_INMEMORY" = "no")
  > test_check("MonetDBLite")
  Loading required package: MonetDBLite
  ── 1. Error: (unknown) (@test_04_dplyr.R#2)  ───────────────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test_04_dplyr.R:2
  2: stop(txt, domain = NA)
  
  [1] "E"
  [1] "H"
  [1] "M"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 279 SKIPPED: 10 FAILED: 1
  1. Error: (unknown) (@test_04_dplyr.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘dplyr’
Error in re-building vignettes:
  ...
Quitting from lines 316-320 (MonteCarlo-Vignette.Rmd) 
Error: processing vignette ‘MonteCarlo-Vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Running examples in ‘moonBook-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rank2group
> ### Title: rank a numeric vector and returns a new ordinal vector
> ### Aliases: rank2group
> 
> ### ** Examples
> 
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(diamonds)
Warning in data(diamonds) : data set ‘diamonds’ not found
> diamonds$PriceGroup=rank2group(diamonds$price,4)
Error in rank2group(diamonds$price, 4) : object 'diamonds' not found
Execution halted
Package required but not available: ‘rgl’

Packages suggested but not available for checking: ‘car’ ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tidyverse’ ‘tidyr’ ‘dplyr’ ‘ggplot2’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  ── 1. Error: life.table does the mathing correctly (@test_analytical_functions_c
  there is no package called 'dplyr'
  1: expect_true(dplyr::near(single_life_table$dx, schleswig_ma$dx/10, tol = 0.1) %>% 
         all) at testthat/test_analytical_functions_calculations.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: dplyr::near(single_life_table$dx, schleswig_ma$dx/10, tol = 0.1) %>% all
  5: eval(lhs, parent, parent)
  6: eval(lhs, parent, parent)
  7: dplyr::near
  8: getExportedValue(pkg, name)
  9: asNamespace(ns)
  10: getNamespace(ns)
  11: tryCatch(loadNamespace(name), error = function(e) stop(e))
  12: tryCatchList(expr, classes, parentenv, handlers)
  13: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  14: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 73 SKIPPED: 0 FAILED: 1
  1. Error: life.table does the mathing correctly (@test_analytical_functions_calculations.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: bitops
Quitting from lines 17-19 (mortAAR_vignette-1.Rmd) 
Error: processing vignette ‘mortAAR_vignette-1.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Packages required but not available: ‘mosaicCore’ ‘mosaic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘mosaic’ ‘ggformula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘mosaic’ ‘ggplot2’ ‘dplyr’
Running examples in ‘mosaicData-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: SnowGR
> ### Title: Snowfall data for Grand Rapids, MI
> ### Aliases: SnowGR
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(SnowGR)
> if (require(mosaic)) {
+   favstats(SnowGR$Total)
+   histogram(~Total, data=SnowGR)
+   xyplot(Total ~ SeasonStart, SnowGR, type=c('p','smooth'))
+ }
Loading required package: mosaic
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mosaic’
> if (require(reshape2)) {
+   Snow2 <- melt(SnowGR, id=1:2)
+   names(Snow2)[3:4] <- c('Time','Snow')
+   bwplot(Snow ~ Time, Snow2)
+ }
Loading required package: reshape2
Error in bwplot(Snow ~ Time, Snow2) : could not find function "bwplot"
Execution halted
Packages required but not available:
  ‘mosaicCore’ ‘dplyr’ ‘caret’ ‘ggplot2’ ‘ggformula’ ‘tibble’ ‘tidyr’
  ‘tidyverse’

Package suggested but not available for checking: ‘mosaic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggformula’ ‘mosaicCore’ ‘ggplot2’ ‘tidyr’ ‘readr’ ‘ggdendro’
  ‘broom’

Packages suggested but not available for checking: ‘fastR’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.2-20, (SVN revision 725)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.0.1, April 1st, 2018, [PJ_VERSION: 501]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-7 
Warning in .local(x, y, time, data, proj, ...) :
  There were NA locations detected and omitted. Currently they are not stored in unusedrecords
Loading required package: ggmap
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggmap’
Loading required package: mapproj
Loading required package: maps

Error: processing vignette ‘move.Rnw’ failed with diagnostics:
 chunk 15 (label = googleplot) 
Error in ggmap(m) : could not find function "ggmap"
Execution halted
Packages required but not available: ‘ggplot2’ ‘RStoolbox’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘matlib’
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘mvoutlier’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  weiszfeldIterations.cpp:195:48: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Mposterior.Rcheck/00install.out’ for details.
Package required but not available: ‘tables’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Packages suggested but not available for checking: ‘geojsonio’ ‘rmapshaper’

Package which this enhances but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘mrMLM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/MSBVAR.Rcheck/00install.out’ for details.
Package required but not available: ‘cellranger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘hydroPSO’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mscstexta4r’
Package required but not available: ‘xcms’

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MSeasy’

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘ggplot2’
Running examples in ‘MSG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: canabalt
> ### Title: The scores of the game Canabalt from Twitter
> ### Aliases: canabalt
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘poio’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘Rssa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘car’
Running examples in ‘mthapower-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mthapower
> ### Title: Post-hoc power calculations - mtDNA haplogroups
> ### Aliases: mthapower
> 
> ### ** Examples
> 
> # Example 1:
> pow <- mthapower(n.cases=203, p0=0.443, Nh=13, OR.cas.ctrl=2.33, sig.level=0.05)
> 
> # Example 2:
> # Create data frames
> pow.H150 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.5, sig.level=0.05)
> pow.H175 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=1.75, sig.level=0.05)
> pow.H200 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2, sig.level=0.05)
> pow.H250 <- mthapower(n.cases=seq(50,1000,by=50), p0=0.433, Nh=11,
+                       OR.cas.ctrl=2.5, sig.level=0.05)
> 
> # Bind the three data frames:
> bindata <- rbind(pow.H150,pow.H175,pow.H200,pow.H250)
> # Adds column OR to binded data frame:
> bindata$OR <- rep(factor(c(1.50,1.75,2,2.5)),
+               times = c(nrow(pow.H150),
+                         nrow(pow.H175),
+                         nrow(pow.H200),
+                         nrow(pow.H250)))
> # Create plot:
> # install.packages("car")
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tibble’ ‘readr’ ‘tidyr’ ‘tidyselect’

Package suggested but not available for checking: ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DiagrammeR’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘chfls1.Rnw’ failed with diagnostics:
 chunk 1 (label = setup) 
Error in library("car") : there is no package called ‘car’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 121-130 (SIR-MCMC.Rmd) 
Error: processing vignette ‘SIR-MCMC.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Depends: includes the non-default packages:
  ‘car’ ‘pdist’ ‘pls’ ‘gplots’ ‘mvtnorm’ ‘robustbase’ ‘gtools’ ‘bitops’
  ‘caTools’ ‘pcaPP’ ‘rrcov’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘cplm’
Running examples in ‘munsell-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chroma_slice
> ### Title: Plot all colours with the same chroma
> ### Aliases: chroma_slice
> 
> ### ** Examples
> 
> chroma_slice(2)
Error: ggplot2 needed for this function to work. Please install it.
Execution halted
Running examples in ‘musica-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: compare
> ### Title: Compare decomposed variables
> ### Aliases: compare
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 17-20 (using_musica.Rmd) 
Error: processing vignette ‘using_musica.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘mutoss-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Qvalue
> ### Title: Storey's (2001) q-value Procedure...
> ### Aliases: Qvalue
> 
> ### ** Examples
> pval <- c(runif(50), runif(50, 0, 0.01))
> result <- Qvalue(pval)
Loading required package: qvalue
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘qvalue’
Package qvalue is required - should we install it?
Error in requireLibrary("qvalue") : 
  Required package qvalue should not be installed
Calls: Qvalue -> requireLibrary
Execution halted
Package required but not available: ‘rattle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘heplots’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: corpcor
Loading required package: subplex
##
## mvMORPH package (1.0.9)
## Multivariate evolutionary models
##
## See the tutorials: browseVignettes("mvMORPH")
##
## To cite package 'mvMORPH': citation("mvMORPH")
##
Done.
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Done.
Quitting from lines 326-349 (tutorial_mvMORPH.Rmd) 
Error: processing vignette ‘tutorial_mvMORPH.Rmd’ failed with diagnostics:
could not find function "ellipse"
Execution halted
Packages required but not available: ‘mvoutlier’ ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘robCompositions’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘mvQuad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot (plot.NIGrid)
> ### Title: plots an NIGrid-object
> ### Aliases: 'plot (plot.NIGrid)' plot.NIGrid
> 
> ### ** Examples
> 
> myGrid <- createNIGrid(dim=4, type=c("GHe", "cNC1", "GLe", "oNC1"),
+                        level=c(3,4,5,6))
> plot(myGrid) ## dimension 1-min(3,dim(myGrid)) are plotted
Error in plot.NIGrid(myGrid) : 
  wrong dimensions stated to be plotted (no 'rgl'-package for 3d-plot)
Calls: plot -> plot.NIGrid
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 31-43 (mvtboost_vignette.Rmd) 
Error: processing vignette ‘mvtboost_vignette.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘mwaved-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multiWaveD
> ### Title: Full mWaveD analysis
> ### Aliases: multiWaveD
> 
> ### ** Examples
> 
> library(mwaved)
> # Simulate the multichannel doppler signal.
> m <- 3
> n <- 2^10
> signal <- makeDoppler(n)
> # Noise levels per channel
> e <- rnorm(m * n)
> # Create Gamma blur
> shape <- seq(from = 0.5, to = 1, length = m)
> scale <- rep(0.25, m)
> G <- gammaBlur(n, shape = shape, scale = scale)
> # Convolve the signal
> X <- blurSignal(signal, G)
> # Create error with custom signal to noise ratio
> SNR <- c(10, 15, 20)
> sigma <- sigmaSNR(X, SNR)
> if (requireNamespace("fracdiff", quietly = TRUE)) {
+   alpha <- c(0.75, 0.8, 1)
+ } else {
+   alpha <- rep(1, m)
+ }
> E <- multiNoise(n, sigma, alpha)
> # Create noisy & blurred multichannel signal
> Y <- X + E
> # Compute mWaveD object
> mWaveDObj <- multiWaveD(Y, G = G, alpha = alpha)
> plot(mWaveDObj)
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: plot ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 14-53 (mWaveD.Rmd) 
Error: processing vignette ‘mWaveD.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘biomartr’ ‘dplyr’ ‘taxize’ ‘ggplot2’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘filesstrings’ ‘autothresholdr’ ‘dplyr’ ‘purrr’ ‘detrendr’ ‘ijtiff’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tidyr’ ‘tibble’ ‘visdat’ ‘purrrlyr’
  ‘forcats’ ‘viridis’

Packages suggested but not available for checking:
  ‘wakefield’ ‘vdiffr’ ‘imputeTS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘vsn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘NanoStringNorm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘nat’

Package suggested but not available for checking: ‘rglwidget’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘alphashape3d’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘nat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘openVA’
Packages required but not available: ‘dplyr’ ‘dtplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘nbpMatching’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘heatmaply’ ‘ggplot2’ ‘dendextend’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘car’ ‘Hmisc’ ‘quickPlot’ ‘SpaDES.tools’

Packages suggested but not available for checking: ‘fastshp’ ‘SpaDES.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘netrankr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_rank_intervals
> ### Title: Plot rank intervals
> ### Aliases: plot_rank_intervals
> 
> ### ** Examples
> 
> library(igraph)

Attaching package: ‘igraph’

The following objects are masked from ‘package:stats’:

    decompose, spectrum

The following object is masked from ‘package:base’:

    union

> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

Quitting from lines 70-71 (partial_centrality.Rmd) 
Error: processing vignette ‘partial_centrality.Rmd’ failed with diagnostics:
ggplot2 needed for this function to work. Please install it.
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggvis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘qgraph’ ‘IsingFit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘surveybootstrap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘qgraph’ ‘IsingFit’ ‘ggplot2’ ‘NetworkComparisonTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 11-19 (nifti_basics.Rmd) 
Error: processing vignette ‘nifti_basics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 15-18 (hcp.Rmd) 
Error: processing vignette ‘hcp.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘readr’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggcorrplot’ ‘Hmisc’ ‘caret’

Package suggested but not available for checking: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggpmisc’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘NFPdata’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggthemes’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘rstan’ ‘ggplot2’ ‘tensorflow’
Package required but not available: ‘tibble’

Packages which this enhances but not available for checking:
  ‘kokudosuuchi’ ‘estatapi’ ‘jpndistrict’ ‘jpmesh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘vpc’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘qdap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘dplyr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘ggplot2’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘Hmisc’
Running examples in ‘nLTT-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: get_nltt_values
> ### Title: Collects the nLTT values of all phylogenies in the
> ###   melted/uncast/long form
> ### Aliases: get_nltt_values
> 
> ### ** Examples
> 
>   library(ape)
>   library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 60-65 (get_nltt_values.Rmd) 
Error: processing vignette ‘get_nltt_values.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘d3heatmap’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘thief’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘choroplethr’ ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘hurricaneexposure’ ‘tidyr’
  ‘viridis’

Packages suggested but not available for checking:
  ‘hurricaneexposuredata’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘dplyr’ ‘ggplot2’ ‘ggmap’ ‘ggExtra’ ‘tcR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘readr’ ‘dplyr’

Packages suggested but not available for checking: ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘metaplot’

Package suggested but not available for checking: ‘wrangle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
This is lavaan 0.6-1
lavaan is BETA software! Please report any bugs.
This is nonnest2 0.5-1.
nonnest2 has not been tested with all combinations of model classes.
Quitting from lines 64-65 (nonnest2.Rmd) 
Error: processing vignette ‘nonnest2.Rmd’ failed with diagnostics:
no applicable method for ‘estfun’ applied to an object of class "lavaan"
Execution halted
Packages required but not available: ‘Hmisc’ ‘rms’

Depends: includes the non-default packages:
  ‘lpSolve’ ‘gdata’ ‘Hmisc’ ‘rms’ ‘geometry’ ‘psych’ ‘pwt’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotly’ ‘ggplot2’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ez’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readxl’ ‘RVAideMemoire’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘agricolae’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘etl’ ‘dplyr’

Packages suggested but not available for checking: ‘dbplyr’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggthemes’ ‘GGally’ ‘forcats’
Running examples in ‘nzelect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GE2014
> ### Title: General Election Results 2014
> ### Aliases: GE2014
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # the following matches the results published at
> # http://www.electionresults.govt.nz/electionresults_2014/e9/html/e9_part1.html
> library(tidyr)
Error in library(tidyr) : there is no package called ‘tidyr’
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(nzelect)
  > 
  > test_check("nzelect")
  ── 1. Error: (unknown) (@test_totals_v_published2014.R#8)  ─────────────────────
  object 'Party' not found
  1: expect_equal(sum(filter(GE2014, Party == "National Party" & VotingType == "Party")$Votes), 
         1131501) at testthat/test_totals_v_published2014.R:8
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: filter(GE2014, Party == "National Party" & VotingType == "Party")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_totals_v_published2014.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘AGread’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plot3Drgl’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘marmap’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 119-127 (oecd_vignette_main.Rmd) 
Error: processing vignette ‘oecd_vignette_main.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘tibble’ ‘ggplot2’
Packages required but not available:
  ‘car’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘recipes’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘caret’ ‘descriptr’ ‘haven’ ‘readr’ ‘readxl’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ompr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readr’ ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘haven’ ‘feather’
Package required but not available: ‘mlr’

Package suggested but not available for checking: ‘farff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘InSilicoVA’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [14s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nlme
This is mgcv 1.8-23. For overview type 'help("mgcv-package")'.
Quitting from lines 92-96 (opera-vignette.Rmd) 
Error: processing vignette ‘opera-vignette.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Package required but not available: ‘DepthProc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘optiSolve’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
        user system elapsed
optrdd 4.817  0.101   7.056
Packages suggested but not available for checking: ‘caret’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 84-103 (ordinalClust.Rmd) 
Error: processing vignette ‘ordinalClust.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [11s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(origami)
  origami: Generalized Cross-Validation Framework
  Version: 1.0.0
  > library(data.table)
  > test_check("origami")
  ── 1. Error: (unknown) (@test-overall_timeseries.R#1)  ─────────────────────────
  there is no package called 'forecast'
  1: library(forecast) at testthat/test-overall_timeseries.R:1
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 24 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-overall_timeseries.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 286-321 (generalizedCV.Rmd) 
Error: processing vignette ‘generalizedCV.Rmd’ failed with diagnostics:
there is no package called 'forecast'
Execution halted
Package required but not available: ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘keras’ ‘pROC’
Error in re-building vignettes:
  ...
Loading required package: knitcitations
Loading required package: OSTSC
Loading required package: keras
Loading required package: dummies
dummies-1.5.6 provided by Decision Patterns

Loading required package: pROC
Quitting from lines 518-526 (Over_Sampling_for_Time_Series_Classification.Rmd) 
Error: processing vignette ‘Over_Sampling_for_Time_Series_Classification.Rmd’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘forcats’ ‘HDoutliers’ ‘cellWise’ ‘GGally’

Package suggested but not available for checking: ‘mbgraphic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘AER’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggiraph’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 98-112 (intro.Rmd) 
Error: processing vignette ‘intro.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘pagenum-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pagenum
> ### Title: Put Page Numbers on Graphics
> ### Aliases: pagenum setPagenum getPagenum setPagenum getPagenum
> 
> ### ** Examples
> 
> # base graphics
> setPagenum(1)
> plot(Sepal.Length~Sepal.Width, data=iris, col=Species, pch=19)
> pagenum()
> 
> # lattice, date
> setPagenum(getPagenum()+1) # Manual increment
> require(lattice)
Loading required package: lattice
> xyplot(Sepal.Length~Sepal.Width, data=iris, groups=Species)
> pagenum(date=TRUE)
> 
> # ggplot2, top-right
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> ggplot(iris, aes(x=Sepal.Width, y=Sepal.Length,
+   color=Species)) + geom_point() + theme_classic()
Error in ggplot(iris, aes(x = Sepal.Width, y = Sepal.Length, color = Species)) : 
  could not find function "ggplot"
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pagenum)
  > 
  > test_check("pagenum")
  ── 1. Error: (unknown) (@test_pagenum.R#17)  ───────────────────────────────────
  could not find function "ggplot"
  1: .handleSimpleError(function (e) 
     {
         handled <<- TRUE
         test_error <<- e
         options(expressions = expressions_opt_new)
         on.exit(options(expressions = expressions_opt), add = TRUE)
         e$expectation_calls <- frame_calls(11, 2)
         test_error <<- e
         register_expectation(e)
         e$handled <- TRUE
         test_error <<- e
     }, "could not find function \"ggplot\"", quote(ggplot(iris, aes(x = Sepal.Width, 
         y = Sepal.Length, color = Species)))) at testthat/test_pagenum.R:17
  2: eval(code, test_env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_pagenum.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 74-79 (pagenum_examples.Rmd) 
Error: processing vignette ‘pagenum_examples.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘mcprofile’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘agricolae’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘paleomorph-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotSpecimens
> ### Title: Plot an array of specimen landmark data in an interactive 3D
> ###   frame
> ### Aliases: plotSpecimens
> 
> ### ** Examples
> 
> A <- array(rep(rnorm(3 * 20, sd = 30), by = 6) + rnorm(6 * 20 * 3), 
+        dim = c(20, 3, 6))
> plotSpecimens(A)
Error: Package rgl needed for this function to work. Please install it with install.packages('rgl').
Execution halted
Running examples in ‘palettetown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scale_colour_poke
> ### Title: Add a pokemon palette to a ggplot2 colour or fill scale.
> ### Aliases: scale_color_poke scale_colour_poke scale_fill_poke
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘FactoClass’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘lmerTest’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘tables’ ‘rms’ ‘forecast’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (pander.Rmd) 
Error: processing vignette ‘pander.Rmd’ failed with diagnostics:
there is no package called 'tables'
Execution halted
Packages required but not available: ‘oai’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘parallelDist.Rnw’ failed with diagnostics:
 chunk 2 (label = performanceDtw) 
Error in ggplot(data = comparison, aes(x = expr, y = min, group = method,  : 
  could not find function "ggplot"
Execution halted
Packages suggested but not available for checking: ‘GGally’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 26-34 (Simulating-Power.Rmd) 
Error: processing vignette ‘Simulating-Power.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘hansard’ ‘mnis’ ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘leaflet’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘PartCensReg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Cens.SMN.PCR
> ### Title: Estimation and diagnostics for partially linear censored
> ###   regression models
> ### Aliases: Cens.SMN.PCR
> ### Keywords: package censored censoring diagnostic partial partially
> 
> ### ** Examples
> 
> dtawage = get(data(PSID1976,package = "AER"))
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: get -> data -> find.package
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘egcm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘partialAR’ ‘ggplot2’

Package suggested but not available for checking: ‘egcm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidygraph’ ‘dplyr’

Package suggested but not available for checking: ‘ggraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘regtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘DT’ ‘ggplot2’ ‘tidyverse’ ‘gapminder’
Error in re-building vignettes:
  ...
Quitting from lines 32-39 (passport.Rmd) 
Error: processing vignette ‘passport.Rmd’ failed with diagnostics:
there is no package called 'gapminder'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 209-220 (getting-started.Rmd) 
Error: processing vignette ‘getting-started.Rmd’ failed with diagnostics:
there is no package called 'tidyr'
Execution halted
Package required but not available: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Morpho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘PBImisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: flu
> ### Title: Numbers of flu occurences in the 10 years period in the Poland.
> ### Aliases: flu
> ### Keywords: flu
> 
> ### ** Examples
> 
> data(flu)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘phylosim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘plotly’ ‘qpcR’ ‘visdat’

Packages suggested but not available for checking: ‘dplyr’ ‘RDML’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘readr’ ‘ggplot2’ ‘broom’

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘strvalidator’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking: ‘adabag’ ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <rsnak>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  failed to tidy R code in chunk <testit>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 734-750 (PDQutils.Rnw) 
Error: processing vignette ‘PDQutils.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘car’ ‘coefplot’ ‘papeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘viridis’ ‘ggthemes’
Running examples in ‘PeakError-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: PeakError
> ### Title: PeakError
> ### Aliases: PeakError
> 
> ### ** Examples
> 
> x <- seq(5, 85, by=5)
> peaks <- rbind(Peaks("chr2", x, x+3),
+                Peaks("chr3", c(25, 38, 57), c(33, 54, 75)),
+                Peaks("chr4", c(5, 32, 38, 65), c(15, 35, 55, 85)),
+                Peaks("chr5", c(12, 26, 56, 75), c(16, 54, 59, 85)))
> regions <- NULL
> for(chr in 1:5){
+   regions <- rbind(regions, {
+     data.frame(chrom=paste0("chr", chr),
+                chromStart=c(10, 30, 50, 70),
+                chromEnd=c(20, 40, 60, 80),
+                annotation=c("noPeaks", "peakStart", "peakEnd", "peaks"))
+   })
+ }
> err <- PeakError(peaks, regions)
> ann.colors <-
+   c(noPeaks="#f6f4bf",
+     peakStart="#ffafaf",
+     peakEnd="#ff4c4c",
+     peaks="#a445ee")
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘penaltyLearning’
Running examples in ‘PeakSegDP-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chr11ChIPseq
> ### Title: ChIP-seq aligned read coverage for 4 samples on a subset of
> ###   chr11
> ### Aliases: chr11ChIPseq
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(chr11ChIPseq)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘penaltyLearning’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rms’

Packages suggested but not available for checking: ‘riskRegression’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘car’ ‘spsurvey’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotHD
> ### Title: Histogram and density plot
> ### Aliases: plotHD
> ### Keywords: dplot
> 
> ### ** Examples
> 
> x <- rnorm(100, 10, 2)
> plotHD(x, HD = "stack")
Error: Package 'car' needed for this function to work. Please install it.
Execution halted
Package required but not available: ‘adegenet’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘pacotest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘broom’ ‘tidyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘PerformanceAnalytics-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Omega
> ### Title: calculate Omega for a return series
> ### Aliases: Omega
> 
> ### ** Examples
> 
> 
>     data(edhec)
>     Omega(edhec)
               Convertible Arbitrage CTA Global Distressed Securities
Omega (L = 0%)              2.602138   1.936841              3.230443
               Emerging Markets Equity Market Neutral Event Driven
Omega (L = 0%)         1.765435              6.213714     2.999655
               Fixed Income Arbitrage Global Macro Long/Short Equity
Omega (L = 0%)               2.585943     3.516616          2.438064
               Merger Arbitrage Relative Value Short Selling Funds of Funds
Omega (L = 0%)         4.595886       3.815368      1.228785       2.460153
>     Omega(edhec[,13],method="interp",output="point")
Error in FUN(newX[, i], ...) : 
  requireNamespace("Hmisc", quietly = TRUE) is not TRUE
Calls: Omega -> apply -> FUN -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric


Attaching package: ‘PerformanceAnalytics’

The following object is masked from ‘package:graphics’:

    legend


Attaching package: ‘gplots’

The following object is masked from ‘package:PerformanceAnalytics’:

    textplot

The following object is masked from ‘package:stats’:

    lowess


Error: processing vignette ‘textplotPresentation-CRUG-2011.Rnw’ failed with diagnostics:
 chunk 5 (label = Hmiscformat) 
Error in library(Hmisc) : there is no package called ‘Hmisc’
Execution halted
Package required but not available: ‘seriation’

Packages suggested but not available for checking:
  ‘dendextend’ ‘dendextendRcpp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘viridis’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘car’ ‘rms’
Running examples in ‘perturb-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: perturb
> ### Title: Perturbation analysis to evaluate collinearity
> ### Aliases: perturb summary.perturb print.summary.perturb
> ### Keywords: regression
> 
> ### ** Examples
> 
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Packages required but not available: ‘tibble’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘leaflet’ ‘plotly’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
              user system elapsed
AIC.phmm     4.749  0.031   6.142
phmm         3.908  0.000   5.744
phmm-package 3.755  0.008   5.267
Packages suggested but not available for checking: ‘readr’ ‘ggplot2’
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggspectra’ ‘photobiologyWavebands’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘photobiology’ ‘tibble’ ‘dplyr’ ‘tidyr’ ‘readr’ ‘readxl’ ‘hyperSpec’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggspectra’ ‘photobiologyWavebands’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  ‘ggspectra’ ‘photobiologyWavebands’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  ‘photobiologyWavebands’ ‘ggspectra’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘photobiology’ ‘photobiologyWavebands’

Packages suggested but not available for checking: ‘ggplot2’ ‘ggspectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’

Package suggested but not available for checking: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

Packages suggested but not available for checking:
  ‘photobiologyWavebands’ ‘ggplot2’ ‘ggspectra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘photobiology’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [5s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(phrasemachine)
  phrasemachine: Simple Phrase Extraction
  Version 1.1.2 created on 2017-05-29.
  copyright (c) 2016, Matthew J. Denny, Abram Handler, Brendan O'Connor.
  Type help('phrasemachine') or
  vignette('getting_started_with_phrasemachine') to get started.
  Development website: https://github.com/slanglab/phrasemachine
  > 
  > test_check("phrasemachine")
  ── 1. Error: See if tagging five documents works, and if coarsening works (@test
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_POS_tag_documents.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ── 2. Error: See if extractor works (@test_extract_phrases.R#5)  ───────────────
  there is no package called 'quanteda'
  1: quanteda::data_corpus_inaugural at testthat/test_extract_phrases.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  Currently tagging document 1 of 1 
  Extracting phrases from document 1 of 1 
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error: See if tagging five documents works, and if coarsening works (@test_POS_tag_documents.R#5) 
  2. Error: See if extractor works (@test_extract_phrases.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 82-91 (getting_started_with_phrasemachine.Rmd) 
Error: processing vignette ‘getting_started_with_phrasemachine.Rmd’ failed with diagnostics:
there is no package called 'quanteda'
Execution halted
Package suggested but not available for checking: ‘OutbreakTools’
Package required but not available: ‘RNeXML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘drc’ ‘geomorph’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rphylopars’
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘ggraph’ ‘purrr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘phyloseq’ ‘ggnetwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘NHPoisson’ ‘phylobase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 16-43 (IdealWeightComparison.Rmd) 
Error: processing vignette ‘IdealWeightComparison.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking:
  ‘tidyverse’ ‘pinnacle.API’ ‘Lahman’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘modelr’ ‘tidyverse’
Error in re-building vignettes:
  ...
Quitting from lines 119-141 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'tidyverse'
Execution halted
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘ggsubplot’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dbplyr’ ‘purrr’ ‘tidyselect’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘broom’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggnetwork’ ‘ggplot2’ ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ReportingTools’
Package required but not available: ‘ggplot2’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘cowplot’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘BradleyTerryScalable’ ‘StatRank’ ‘kableExtra’ ‘tibble’
Packages required but not available: ‘dplyr’ ‘ggdendro’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘latticist’ ‘ggplot2’
Packages required but not available: ‘dplyr’ ‘dbplyr’ ‘gistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘AER’ ‘car’ ‘clusterSEs’
Running examples in ‘plm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: vcovBK
> ### Title: Beck and Katz Robust Covariance Matrix Estimators
> ### Aliases: vcovBK vcovBK.plm
> ### Keywords: regression
> 
> ### ** Examples
> 
> library(lmtest)
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric


Error: processing vignette ‘plm.rnw’ failed with diagnostics:
 chunk 46 
Error in library("car") : there is no package called 'car'
Execution halted
Found the following significant warnings:
  cat_pair.c:64:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  cat_pair.c:79:17: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/PLordprob.Rcheck/00install.out’ for details.
Package required but not available: ‘aqp’

Packages suggested but not available for checking:
  ‘adehabitat’ ‘spcosa’ ‘rgbif’ ‘Hmisc’ ‘GSIF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’

Package suggested but not available for checking: ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘tibble’ ‘crosstalk’ ‘purrr’

Packages suggested but not available for checking:
  ‘ggthemes’ ‘GGally’ ‘broom’ ‘dendextend’ ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘mixOmics’ ‘SensoMineR’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

The following object is masked from ‘package:stats’:

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Packages suggested but not available for checking: ‘FactoMineR’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 310-329 (plspm_introduction.Rnw) 
Error: processing vignette ‘plspm_introduction.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘coreSim’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Packages suggested but not available for checking: ‘DT’ ‘styler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘xpose’ ‘GGally’ ‘PKNCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readr’ ‘dplyr’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘SmarterPoland’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘TripleR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘weights’ ‘ENmisc’ ‘car’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Packages suggested but not available for checking:
  ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘DT’

Package suggested but not available for checking: ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MDSMap’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mixOmics’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘ggplot2’ ‘pegas’ ‘mmod’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’

Package suggested but not available for checking: ‘Lahman’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘adegenet’ ‘ggplot2’ ‘pegas’ ‘dplyr’

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘poppr’ ‘readxl’

Package suggested but not available for checking: ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

Error: processing vignette ‘burkina-faso-females.Rnw’ failed with diagnostics:
 chunk 1 (label = sweave-setup) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘PortfolioEffectHFT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘lmerTest’ ‘ggplot2’ ‘ggsci’ ‘viridis’
Running ‘testthat.R’ [0s/0s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Error in re-building vignettes:
  ...
You are recommended to install the tinytex package to build PDF.FALSE
Latexmk: This is Latexmk, John Collins, 1 January 2015, version: 4.41.
File::Glob::glob() will disappear in perl 5.30. Use File::Glob::bsd_glob() instead. at /usr/bin/latexmk line 7482.
Quitting from lines 197-200 (three-level.Rmd) 
Error: processing vignette ‘three-level.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package suggested but not available for checking: ‘factoextra’
Error in re-building vignettes:
  ...
Quitting from lines 45-48 (fcm.Rmd) 
Error: processing vignette ‘fcm.Rmd’ failed with diagnostics:
there is no package called 'factoextra'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘leaflet’ ‘PakPC2017’ ‘tidyr’ ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘GGally’ ‘ggplot2’ ‘PPtreeViz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘doBy’
Packages required but not available: ‘precrec’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  ‘AER’ ‘caret’ ‘sampleSelection’
Packages required but not available: ‘caret’ ‘forecast’ ‘TSPred’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 31-62 (prepplotOverview.Rmd) 
Error: processing vignette ‘prepplotOverview.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Package required but not available: ‘caret’

Packages suggested but not available for checking: ‘ggplot2’ ‘preproviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘caret’

Packages suggested but not available for checking: ‘preprocomb’ ‘preproviz’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’ ‘ggdendro’

Package suggested but not available for checking: ‘preprocomb’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quanteda’ ‘ggplot2’ ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 50-91 (interpolation-in-small-samples.Rmd) 
Error: processing vignette ‘interpolation-in-small-samples.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 154-155 (prioritylasso_vignette.Rmd) 
Error: processing vignette ‘prioritylasso_vignette.Rmd’ failed with diagnostics:
there is no package called 'pROC'
Execution halted
Packages required but not available:
  ‘bupaR’ ‘processmapR’ ‘dplyr’ ‘tidyr’ ‘DiagrammeR’

Package suggested but not available for checking: ‘edeaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘bupaR’ ‘edeaR’ ‘DiagrammeR’ ‘ggplot2’ ‘ggthemes’ ‘purrr’
  ‘forcats’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘bupaR’ ‘edeaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rfigshare’
Running examples in ‘ProFound-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: FPtest
> ### Title: False Positive Reference Data
> ### Aliases: FPtest
> ### Keywords: datasets
> 
> ### ** Examples
> 
> image=readFITS(system.file("extdata", 'VIKING/mystery_VIKING_Z.fits', package="ProFound"))
> profound=profoundProFound(image, magzero=30, rotstats=TRUE)
Error: The imager package is needed for this function to work. Please install it from CRAN.
Execution halted
Packages required but not available: ‘ggplot2’ ‘GeneralizedUmatrix’

Package suggested but not available for checking: ‘DataVisualizations’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘incidence’ ‘ggplot2’

Package suggested but not available for checking: ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘readxl’ ‘tibble’
Packages required but not available: ‘rstan’ ‘rstanarm’ ‘ggplot2’

Package suggested but not available for checking: ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘rstan’ ‘tidyr’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘ggdendro’ ‘plotly’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘hyperSpec’
Error in re-building vignettes:
  ...

Error: processing vignette ‘PRROC.Rnw’ failed with diagnostics:
 chunk 47 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘PogromcyDanych’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Hmisc’ ‘ggplot2’
Running examples in ‘pscl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hurdletest
> ### Title: Testing for the Presence of a Zero Hurdle
> ### Aliases: hurdletest
> ### Keywords: regression
> 
> ### ** Examples
> 
> data("bioChemists", package = "pscl")
> fm <- hurdle(art ~ ., data = bioChemists, dist = "negbin", zero = "negbin")
> hurdletest(fm)
Loading required namespace: car
Failed with error:  ‘there is no package called ‘car’’
Error in hurdletest(fm) : requireNamespace("car") is not TRUE
Calls: hurdletest -> stopifnot
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric


Error: processing vignette ‘countreg.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library("car") : there is no package called ‘car’
Execution halted
Packages required but not available: ‘DataCombine’ ‘rio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 403-408 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘tibble’ ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘tidyr’ ‘purrr’ ‘qgraph’ ‘ggcorrplot’ ‘rstanarm’
  ‘lmerTest’ ‘emmeans’ ‘broom’ ‘tibble’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘likert’
Packages required but not available: ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggdendro’ ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘papeR’ ‘rmdformats’

Package suggested but not available for checking: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘pec’ ‘riskRegression’ ‘rms’
Running examples in ‘Publish-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: publish.CauseSpecificCox
> ### Title: Tabulizing cause-specific hazard ratio from all causes with
> ###   confidence limits and Wald test p-values.
> ### Aliases: publish.CauseSpecificCox
> 
> ### ** Examples
> 
> library(riskRegression)
Error in library(riskRegression) : 
  there is no package called ‘riskRegression’
Execution halted
Running ‘test-glmSeries.R’ [2s/4s]
  Running ‘test-publish-gls.R’ [3s/4s]
  Running ‘test-publish-mi.R’ [2s/3s]
Running the tests in ‘tests/test-publish-mi.R’ failed.
Complete output:
  > library(testthat)
  > library(Publish)
  Loading required package: prodlim
  > library(mitools)
  > library(smcfcs)
  > library(riskRegression)
  Error in library(riskRegression) : 
    there is no package called 'riskRegression'
  Execution halted
Packages required but not available:
  ‘dplyr’ ‘MazamaSpatialUtils’ ‘ggmap’ ‘leaflet’ ‘openair’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘gender’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘FactoClass’ ‘FactoMineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘seriation’ ‘alphahull’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mvoutlier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
there is no package called 'rgl'
Execution halted
Packages required but not available: ‘readr’ ‘sjlabelled’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘GGally’ ‘DT’
Error in re-building vignettes:
  ...
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette ‘wilcox1973.Rmd’ failed with diagnostics:
there is no package called 'DT'
Execution halted
Packages required but not available:
  ‘caret’ ‘dplyr’ ‘ggplot2’ ‘ggrepel’ ‘readr’ ‘pROC’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggrepel’ ‘ggplot2’

Packages suggested but not available for checking: ‘DT’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘GGally’ ‘ggplot2’ ‘rgl’
Running examples in ‘QuantNorm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: connection.matrix
> ### Title: Construct connection matrix for network analysis
> ### Aliases: connection.matrix
> 
> ### ** Examples
> 
> 
> library(network); library(ggplot2); library(sna); library(GGally) #drawing network graph
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.

Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘labelled’

Packages suggested but not available for checking: ‘dplyr’ ‘forcats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘fastshp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘agricolae’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Package suggested but not available for checking: ‘data.tree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 106-111 (R2admb.Rnw) 
Error: processing vignette ‘R2admb.Rnw’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘lmerTest’ ‘ggplot2’ ‘afex’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘doBy’ ‘car’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 78-88 (Performance.Rmd) 
Error: processing vignette ‘Performance.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘hierfstat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 28-32 (preparingData.Rmd) 
Error: processing vignette ‘preparingData.Rmd’ failed with diagnostics:
there is no package called 'tidyr'
Execution halted
Packages required but not available:
  ‘radiant.data’ ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘tibble’ ‘broom’ ‘car’ ‘DT’ ‘readr’

Package suggested but not available for checking: ‘feather’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘radiant.data’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.basics’ ‘NeuralNetTools’ ‘car’ ‘ggplot2’
  ‘data.tree’ ‘tidyr’ ‘dplyr’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.model’ ‘dplyr’ ‘ggplot2’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘radiant.data’ ‘radiant.design’ ‘radiant.basics’ ‘radiant.model’
  ‘radiant.multivariate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘viridis’
Error in re-building vignettes:
  ...
radiomics: Functions for texture analysis of greyscale images.
Enter ?calc_features to see available texture features.
Quitting from lines 172-174 (TextureAnalysis.Rmd) 
Error: processing vignette ‘TextureAnalysis.Rmd’ failed with diagnostics:
there is no package called 'viridis'
Execution halted
Package required but not available: ‘rags2ridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 20-33 (ragtop_convertibles_in_r.Rmd) 
Error: processing vignette ‘ragtop_convertibles_in_r.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘tibble’

Packages suggested but not available for checking:
  ‘dplyr’ ‘forcats’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hdrcde’

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: sp

Attaching package: 'raster'

The following object is masked from 'package:SDMTools':

    distance

Quitting from lines 36-40 (raincpc_demo.Rmd) 
Error: processing vignette ‘raincpc_demo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘dplyr’ ‘purrr’
Error in re-building vignettes:
  ...
Quitting from lines 24-40 (intro-to-altmetric.Rmd) 
Error: processing vignette ‘intro-to-altmetric.Rmd’ failed with diagnostics:
there is no package called 'purrr'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘dtplyr’ ‘DT’ ‘GGally’ ‘ggplot2’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pec’
Packages suggested but not available for checking: ‘dplyr’ ‘blockTools’
Error in re-building vignettes:
  ...
Quitting from lines 358-376 (randomizr_vignette.Rmd) 
Error: processing vignette ‘randomizr_vignette.Rmd’ failed with diagnostics:
there is no package called 'blockTools'
Execution halted
Package required but not available: ‘alphahull’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rankhazard-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankhazard-package
> ### Title: Rank-hazard plots
> ### Aliases: rankhazard-package rankhazard
> ### Keywords: package hplot survival
> 
> ### ** Examples
> 
> library(survival)
> model <- coxph(Surv(time,status) ~ age + sex + ph.karno, data = cancer, x=TRUE)
> rankhazardplot(model, data=cancer)
Y-axis range:  0.608 1.49 
 
Relative hazards for each covarite: 
          Min. 1st Qu. Median 3rd Qu. Max.
age      0.743   0.917      1    1.08 1.27
sex      0.608   0.608      1    1.00 1.00
ph.karno 0.766   0.875      1    1.07 1.49
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Packages required but not available: ‘hypervolume’ ‘ggplot2’

Packages suggested but not available for checking:
  ‘dplyr’ ‘gurobi’ ‘rgurobi’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pROC’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rattle’
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘dplyr’

Packages suggested but not available for checking:
  ‘arulesViz’ ‘biclust’ ‘doBy’ ‘ggdendro’ ‘ggraptR’ ‘Hmisc’ ‘odfWeave’
  ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ChainLadder’ ‘FinCal’ ‘Lahman’ ‘nycflights13’ ‘tidyverse’
Package required but not available: ‘refGenome’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rstan’ ‘bayesplot’ ‘ggplot2’ ‘dplyr’

Packages suggested but not available for checking: ‘tidyverse’ ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘readr’

Package suggested but not available for checking: ‘spdplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘dplyr’

Package suggested but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘gistr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘forestFloor’
Package required but not available: ‘rccmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Wed May 23 04:36:41 AM 2018 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
Package required but not available: ‘hdrcde’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘aspace’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘mudata2’ ‘dplyr’ ‘readr’ ‘tibble’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘Hmisc’ ‘haven’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘BCA’ ‘car’ ‘RcmdrMisc’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘biclust’ ‘iBBiG’ ‘superbiclust’ ‘rqubic’ ‘s4vd’ ‘BiBitR’ ‘Rcmdr’
  ‘viridis’

Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ez’ ‘Rcmdr’ ‘RcmdrMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘forecast’

Depends: includes the non-default packages:
  ‘Rcmdr’ ‘TeachingDemos’ ‘tseries’ ‘abind’ ‘MASS’ ‘xts’ ‘forecast’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking:
  ‘car’ ‘pROC’ ‘tableone’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘FactoMineR’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RcmdrMisc’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘HH’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘ggplot2’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mixlm’ ‘phia’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘RcmdrMisc’ ‘OptimClassifier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rcmdr’

Packages suggested but not available for checking: ‘qgraph’ ‘car’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘demography’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘car’

Depends: includes the non-default packages:
  ‘Rcmdr’ ‘tcltk’ ‘car’ ‘RColorBrewer’ ‘colorspace’ ‘vcd’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Rcmdr’ ‘sutteForecastR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘Rcmdr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RcmdrMisc’ ‘car’

Packages suggested but not available for checking: ‘Hmisc’ ‘readxl’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RVAideMemoire’

Package suggested but not available for checking: ‘FSA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘readr’ ‘DT’ ‘ggplot2’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  cwb/cl/special-chars.c:1771:22: warning: suggest parentheses around assignment used as truth value [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rcqp.Rcheck/00install.out’ for details.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tmap’ ‘ggmap’ ‘readxl’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RCzechia")
  Loading required package: RCzechia
  ── 1. Error: (unknown) (@test-1-data-structures.R#1)  ──────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test-1-data-structures.R:1
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-2-code.R#1)  ─────────────────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test-2-code.R:1
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test-1-data-structures.R#1) 
  2. Error: (unknown) (@test-2-code.R#1) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 27-57 (vignette.Rmd) 
Error: processing vignette ‘vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘oai’ ‘solrium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘AER’

Packages suggested but not available for checking: ‘rdd’ ‘rddtools’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘lpdensity’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘AER’ ‘ggplot2’ ‘rdd’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’

Packages suggested but not available for checking: ‘leaflet’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readr’

Packages suggested but not available for checking:
  ‘DT’ ‘tidyverse’ ‘dplyr’ ‘tidyr’ ‘tibble’ ‘purrr’ ‘repurrrsive’
  ‘nycflights13’ ‘codemetar’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rdi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convertRDI
> ### Title: Convert RDI measures
> ### Aliases: convertRDI
> 
> ### ** Examples
> 
> 
> #create genes
> genes = sample(letters, 10000, replace=TRUE)
> #create sequence annotations
> seqAnnot = data.frame(donor = sample(1:4, 10000, replace=TRUE))
> #calculate RDI
> d = rdi(genes, seqAnnot)
> 
> ##convert RDI to actual 'lfc' estimates and compare
> dtrue = convertRDI(d)$pred
> plot(d, dtrue)
> 
> ##look at SD ranges around lfc estimates
> dtrue = convertRDI(d, calcSD=TRUE)
> 
> ##plot using ggplot2
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggthemes’ ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘readxl’

Packages suggested but not available for checking: ‘qpcR’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette ‘mapDWD.Rmd’ failed with diagnostics:
there is no package called 'leaflet'
Execution halted
Packages required but not available: ‘haven’ ‘readr’ ‘readxl’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cellranger’ ‘readr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘streamR’ ‘readxl’ ‘readODS’

Package suggested but not available for checking: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cellranger’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘statsDK’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘rgl’
Error in re-building vignettes:
  ...
Loading required package: kriging
Quitting from lines 27-33 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette ‘recexcavAAR-vignette-1.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘broom’ ‘tibble’ ‘purrr’ ‘tidyselect’

Packages suggested but not available for checking: ‘caret’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘prevR’
Packages suggested but not available for checking: ‘car’ ‘UsingR’
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘REddyProc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 76-80 (rEDM-coprediction.Rmd) 
Error: processing vignette ‘rEDM-coprediction.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running examples in ‘REEMtree-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: REEMtree
> ### Title: Create a RE-EM tree
> ### Aliases: REEMtree
> ### Keywords: tree models
> 
> ### ** Examples
> 
> data(simpleREEMdata)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID)
> 
> # Estimation allowing for autocorrelation
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID, 
+ 	correlation=corAR1())
> 
> # Random parameters model for the random effects
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1+X|ID)
> 
> # Estimation with a subset
> sub <- rep(c(rep(TRUE, 10), rep(FALSE, 2)), 50)
> REEMresult<-REEMtree(Y~D+t+X, data=simpleREEMdata, random=~1|ID, 
+ 	subset=sub)
> 
> # Dataset from the R library "AER"
> data("Grunfeld", package = "AER")
Error in find.package(package, lib.loc, verbose = verbose) : 
  there is no package called ‘AER’
Calls: data -> find.package
Execution halted
Package required but not available: ‘isva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 83-114 (refinr-vignette.Rmd) 
Error: processing vignette ‘refinr-vignette.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Running examples in ‘ref-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: refdata
> ### Title: subsettable reference to matrix or data.frame
> ### Aliases: refdata derefdata derefdata<- [.refdata [<-.refdata [[.refdata
> ###   [[<-.refdata $.refdata $<-.refdata dim.refdata dimnames.refdata
> ###   row.names.refdata names.refdata print.refdata
> ### Keywords: programming manip
> 
> ### ** Examples
> 
> 
>   ## Simple usage Example
>   x <- cbind(1:5, 5:1)       # take a matrix or data frame
>   rx <- refdata(x)           # wrap it into an refdata object
>   rx                         # see the autoprinting
list()
attr(,"dat")
<environment: 0x5599c8ed74b8>
attr(,"ind")
<environment: 0x5599c8ed7870>
attr(,"class")
[1] "refdata" "matrix" 
>   rm(x)                      # delete original to save memory
>   rx[]                       # extract all data
list()
attr(,"dat")
<environment: 0x5599c8ed74b8>
attr(,"ind")
<environment: 0x5599c8ed7870>
>   rx[-1, ]                   # extract part of data
Error in rx[-1, ] : incorrect number of dimensions
Execution halted
Packages required but not available: ‘tibble’ ‘dplyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘plotly’ ‘refund’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘caret’ ‘semPlot’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (short_intro.Rmd) 
Error: processing vignette ‘short_intro.Rmd’ failed with diagnostics:
there is no package called 'semPlot'
Execution halted
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘keras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘viridis’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 73-96 (restrictions.Rmd) 
Error: processing vignette ‘restrictions.Rmd’ failed with diagnostics:
there is no package called 'tibble'
Execution halted
Package which this enhances but not available for checking: ‘seriation’
Package required but not available: ‘PhaseType’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rcmdr’
Packages required but not available: ‘plotly’ ‘data.tree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘OutbreakTools’ ‘ggplot2’ ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘sparklyr’ ‘ggplot2’ ‘DiagrammeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tibble’

Packages suggested but not available for checking: ‘gapminder’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

Package which this enhances but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testCases.R’ [1s/2s]
Running the tests in ‘tests/testCases.R’ failed.
Complete output:
  > ## test constrained lm, rlm, glm
  > # mixing weights
  > # bootstrap standard errors
  > # models with and without intercept
  > # case weights
  > # constraints on factors and interactions
  > 
  > library(restriktor)
  This is restriktor 0.1-80.711
  restriktor is BETA software! Please report any bugs.
  > n <- 100
  > p <- 4
  > betas = c(0.1,0.2,0.3,0.4,0.5)
  > set.seed(3013073)
  > X <- cbind(mvtnorm:::rmvnorm(n, mean=rep(0,p), sigma=diag(p)), rbinom(n,1,0.5))
  > colnames(X) <- c("x1","x2","x3","x4","f1")
  > z <- X %*% betas        
  > y <- z + rnorm(n)
  > DATA <- data.frame(y, X)
  > 
  > # intercept model
  > model1 <- y ~  1 + x1 + x2 + x3 + x4
  > # no intercept model
  > model2 <- y ~ -1 + x1 + x2 + x3 + x4
  > # intercept model with interaction
  > model3 <- y ~ 1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > # intercept model with interaction
  > model4 <- y ~ -1 + x1*f1 + x2*f1 + x3*f1 + x4*f1
  > 
  > ############################ lm #################################
  > linmod1 <- lm(model1, data = DATA)
  > linmod2 <- lm(model2, data = DATA)
  > linmod3 <- lm(model3, data = DATA)
  > linmod1wt <- lm(model1, data = DATA, weights = abs(rnorm(n)))
  > linmod2wt <- lm(model2, data = DATA, weights = abs(rnorm(n)))
  > linmod1fac <- lm(model3, data = DATA)
  > linmod2fac <- lm(model4, data = DATA)
  > 
  > constraints1 <- 'x1 > 0; x2 > 0; x3 > 0'
  > fit.restr1 <- restriktor(linmod1, constraints1)
  Error in UseMethod("conLM") : 
    no applicable method for 'conLM' applied to an object of class "lm"
  Calls: restriktor
  Execution halted
Packages required but not available: ‘useful’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <single>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: rivr
M1 profile specified. Computing upstream profile
Warning in block_exec(params) :
  failed to tidy R code in chunk <loop>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
Warning in block_exec(params) :
  failed to tidy R code in chunk <reval-single>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
M1 profile specified. Computing upstream profile
Quitting from lines 73-74 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Found the following significant warnings:
  simul.cpp:82:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/revealedPrefs.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘dplyr’ ‘ggplot2’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 29-33 (log_parsing.Rmd) 
Error: processing vignette ‘log_parsing.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘purrr’ ‘readr’ ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘MKmisc’
Running examples in ‘RFLPtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RFLPtools-package
> ### Title: Tools to analyse RFLP-data
> ### Aliases: RFLPtools-package RFLPtools
> ### Keywords: package multivariate cluster
> 
> ### ** Examples
> 
> data(RFLPdata)
> res <- RFLPdist(RFLPdata)
> plot(hclust(res[[1]]), main = "Euclidean distance")
> 
> par(mfrow = c(1,2))
> plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
> RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
> 
> data(RFLPref)
> RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
> 
> 
> library(MKmisc)
Error in library(MKmisc) : there is no package called ‘MKmisc’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: RColorBrewer

Error: processing vignette ‘RFLPtools.Rnw’ failed with diagnostics:
 chunk 5 (label = cor) 
Error in library(MKmisc) : there is no package called ‘MKmisc’
Execution halted
Packages required but not available: ‘ggplot2’ ‘UsingR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘purrr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘DT’ ‘haven’ ‘kableExtra’ ‘readr’ ‘readxl’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘oai’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 87-88 (vignette_RGCCA.Rmd) 
Error: processing vignette ‘vignette_RGCCA.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking:
  ‘agricolae’ ‘Hmisc’ ‘openair’ ‘pmg’ ‘Rcmdr’ ‘rgl’ ‘RGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Packages required but not available: ‘readr’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nonlinearTseries’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘nat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readr’ ‘readxl’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘tibble’ ‘haven’ ‘DT’

Packages suggested but not available for checking:
  ‘plotly’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘haven’ ‘readxl’ ‘tibble’

Packages suggested but not available for checking:
  ‘feather’ ‘readODS’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rms’

Packages suggested but not available for checking: ‘Daim’ ‘pec’ ‘pROC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘solrium’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: rivr
M1 profile specified. Computing upstream profile
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Quitting from lines 96-100 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rJava.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Found the following significant warnings:
  PresenceAndAbsence.cpp:536:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  PresenceAndAbsence.cpp:537:14: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rlda.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘lmerTest’
Package required but not available: ‘Luminescence’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Luminescence’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘geojsonio’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘dplyr’ ‘geojsonio’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘merTools’
Running examples in ‘rmcorr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.rmc
> ### Title: Plot the repeated measures correlation coefficient.
> ### Aliases: plot.rmc
> 
> ### ** Examples
> 
> ## Bland Altman 1995 data
> my.rmc <- rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH, dataset = bland1995)
Warning in rmcorr(participant = Subject, measure1 = PacO2, measure2 = pH,  :
  'Subject' coerced into a factor
> plot(my.rmc, overall = TRUE)
> 
> #using ggplot instead
> ggplot2::ggplot(bland1995, ggplot2::aes(x = PacO2, y = pH, group = factor(Subject),
+       color = factor(Subject))) +
+       ggplot2::geom_point(ggplot2::aes(colour = factor(Subject))) +
+       ggplot2::geom_line(ggplot2::aes(y = my.rmc$model$fitted.values), linetype = 1) 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: pwr
Loading required package: psych
Loading required package: RColorBrewer
Loading required package: plotrix

Attaching package: 'plotrix'

The following object is masked from 'package:psych':

    rescale

Loading required package: rmcorr
Loading required package: lme4
Loading required package: Matrix
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: merTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'merTools'
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat2) :
  'sub' coerced into a factor
Warning in rmcorr(sub, newX, newY, exampleMat3) :
  'sub' coerced into a factor
Quitting from lines 470-519 (Combined_paper_figures.Rmd) 
Error: processing vignette ‘Combined_paper_figures.Rmd’ failed with diagnostics:
could not find function "predictInterval"
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggnetwork’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pegas’ ‘adegenet’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘adabag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘Rmisc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: group.CI
> ### Title: Group Confidence Interval
> ### Aliases: group.CI
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> require(latticeExtra)
Loading required package: latticeExtra
Loading required package: RColorBrewer
> with(group.CI(weight~feed,chickwts),
+  segplot(feed~weight.lower+weight.upper,center=weight.mean)
+ )
> 
> require(Hmisc)
Loading required package: Hmisc
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Hmisc’
> with(group.CI(Temp~Month,airquality),
+  xYplot(Cbind(Temp.mean,Temp.lower,Temp.upper)~numericScale(Month),type="b",ylim=c(60,90))
+ )
Error in xYplot(Cbind(Temp.mean, Temp.lower, Temp.upper) ~ numericScale(Month),  : 
  could not find function "xYplot"
Calls: with -> with.default -> eval -> eval
Execution halted
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘readr’ ‘tidyr’ ‘dplyr’
Error in re-building vignettes:
  ...
Quitting from lines 102-131 (gff-processing.Rmd) 
Error: processing vignette ‘gff-processing.Rmd’ failed with diagnostics:
there is no package called 'readr'
Execution halted
Found the following significant warnings:
  npmpois.c:246:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  rmg.c:335:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/rmp.Rcheck/00install.out’ for details.
Packages required but not available: ‘tidyverse’ ‘purrr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘pdp’ ‘purrr’ ‘tibble’ ‘viridis’

Package suggested but not available for checking: ‘openair’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
This is pdfTeX, Version 3.14159265-2.6-1.40.19 (TeX Live 2018/Debian) (preloaded format=pdflatex)
 restricted \write18 enabled.
entering extended mode
Quitting from lines 208-221 (rte-vignette_creating_exams.Rmd) 
Error: processing vignette ‘rte-vignette_creating_exams.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘rdflib’ ‘rfigshare’ ‘phylobase’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’

Packages suggested but not available for checking:
  ‘dendextend’ ‘DT’ ‘ggdendro’ ‘ggplot2’ ‘leaflet’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘isdparser’

Packages suggested but not available for checking:
  ‘taxize’ ‘leaflet’ ‘purrr’ ‘ggmap’ ‘ropenaq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 39-48 (RNOmni.Rmd) 
Error: processing vignette ‘RNOmni.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘rcrossref’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘car’ ‘GGally’ ‘VIM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘beadarray’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...

 google.com                      


 google.com                      

Quitting from lines 60-62 (using_robotstxt.Rmd) 
Error: processing vignette ‘using_robotstxt.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘GSE’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘GGally’
Error in re-building vignettes:
  ...
Loading required package: robustbase
Loading required package: xtable
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘lmrob_simulation.Rnw’ failed with diagnostics:
 chunk 2 (label = graphics-setup) 
Error in eval(expr, .GlobalEnv) : require(ggplot2) is not TRUE
Execution halted
Packages required but not available: ‘ggplot2’ ‘perry’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Packages suggested but not available for checking: ‘tables’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘data.tree’
Error in re-building vignettes:
  ...

Attaching package: 'rODE'

The following object is masked from 'package:stats':

    step

Quitting from lines 27-65 (ErrorEuler.Rmd) 
Error: processing vignette ‘ErrorEuler.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘tidyr’ ‘alphahull’
Running examples in ‘rollply-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: build_grid_ahull_fill
> ### Title: Regular grid in alpha-hull
> ### Aliases: build_grid_ahull_fill
> 
> ### ** Examples
> 
> 
> data(meadow)
> 
> # Plot a grid with diagnostics
> grid <- build_grid_ahull_fill(meadow[ ,c('lon','lat')], 10000,
+                               grid_opts = list(verbose = TRUE))
Error in build_grid_ahull_fill(meadow[, c("lon", "lat")], 10000, grid_opts = list(verbose = TRUE)) : 
  Alpha-hull-based grids require package alphahull
Execution halted
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rollply)
  > 
  > test_check("rollply")
  ── 1. Error: inahull_cpp works (@test_inahull.R#9)  ────────────────────────────
  there is no package called 'alphahull'
  1: library(alphahull) at testthat/test_inahull.R:9
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 1
  1. Error: inahull_cpp works (@test_inahull.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-27 (rollply.Rmd) 
Error: processing vignette ‘rollply.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘openair’ ‘ggmap’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘someFIGIs.R’ [0s/2s]
Running the tests in ‘tests/someFIGIs.R’ failed.
Complete output:
  > library(ROpenFIGI)
  > jsondf <- data.frame(idType=c("ID_ISIN"),idValue=c("US922646AS37"),
  +                      exchCode=c(NA),currency=NA,micCode=NA,stringsAsFactors = F)
  > 
  > jsonrst <- OpenFIGI(jsondf)
  > jsonrst
  [[1]]
            figi                  name             ticker exchCode compositeFIGI
  1 BBG00004SPH6 REPUBLIC OF VENEZUELA VENZ 9.25 09/15/27  EUROTLX            NA
       uniqueID securityType marketSector shareClassFIGI uniqueIDFutOpt
  1 COTT3359474       GLOBAL         Govt             NA             NA
    securityType2 securityDescription
  1            NA VENZ 9 1/4 09/15/27
  
  > 
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Packages required but not available: ‘mrfDepth’ ‘rrcovHD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘rgl’ ‘sphereplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ftsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RNeXML’ ‘phylobase’ ‘fulltext’ ‘readxl’
Error in re-building vignettes:
  ...
Quitting from lines 148-152 (data_mashups.Rmd) 
Error: processing vignette ‘data_mashups.Rmd’ failed with diagnostics:
there is no package called 'phylobase'
Execution halted
Package required but not available: ‘BioGeoBEARS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rpdo-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pdo
> ### Title: Pacific Decadal Oscillation Index
> ### Aliases: pdo
> ### Keywords: datasets
> 
> ### ** Examples
> 
> library(rpdo)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: parallel
Quitting from lines 7-13 (diagnostics.Rmd) 
Error: processing vignette ‘diagnostics.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rpivotTable)
  > 
  > test_check("rpivotTable")
  ── 1. Error: (unknown) (@test_data.R#3)  ───────────────────────────────────────
  there is no package called 'dplyr'
  1: library(dplyr) at testthat/test_data.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_data.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 103-110 (rpivotTableIntroduction.Rmd) 
Error: processing vignette ‘rpivotTableIntroduction.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘solrium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘leaflet’ ‘mapview’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘dbplyr’
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘rms’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tableone’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘warbleR’ ‘dplyr’ ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RRF.Rcheck/00install.out’ for details.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘plotly’ ‘GGally’

Package suggested but not available for checking: ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘tidyr’ ‘dplyr’ ‘purrr’ ‘tibble’ ‘recipes’

Packages suggested but not available for checking: ‘ggplot2’ ‘AmesHousing’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘rgl’ ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘FactoMineR’ ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘purrr’ ‘tidyselect’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘aire.zmvm’ ‘ggplot2’ ‘ggmap’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘ggplot2’

Packages suggested but not available for checking: ‘kableExtra’ ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘emmeans’
Package suggested but not available for checking: ‘NeuralNetTools’
Package required but not available: ‘sparklyr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bayesplot’ ‘ggplot2’ ‘rstan’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘shinystan’ ‘bayesplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rstan’

Packages suggested but not available for checking: ‘ggplot2’ ‘ggjoy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘bayesplot’ ‘rstan’ ‘rstanarm’ ‘shinystan’ ‘usethis’
Package required but not available: ‘tibble’

Package which this enhances but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘inlmisc’

Packages suggested but not available for checking: ‘leaflet’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘rsvd-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rpca
> ### Title: Randomized principal component analysis (rpca).
> ### Aliases: rpca
> 
> ### ** Examples
> 
> 
> library('rsvd')
> #
> # Load Edgar Anderson's Iris Data
> #
> data('iris')
> 
> #
> # log transform
> #
> log.iris <- log( iris[ , 1:4] )
> iris.species <- iris[ , 5]
> 
> #
> # Perform rPCA and compute only the first two PCs
> #
> iris.rpca <- rpca(log.iris, k=2)
> summary(iris.rpca) # Summary
                         PC1   PC2
Explained variance     2.933 0.907
Standard deviations    1.712 0.952
Proportion of variance 0.733 0.227
Cumulative proportion  0.733 0.960
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952

Eigenvalues:
[1] 2.933 0.907

Rotation:
                PC1    PC2
Sepal.Length -0.504 -0.455
Sepal.Width   0.302 -0.889
Petal.Length -0.577 -0.034
Petal.Width  -0.567 -0.035
> 
> #
> # Use rPCA to compute all PCs, similar to \code{prcomp}
> #
> iris.rpca <- rpca(log.iris)
> summary(iris.rpca) # Summary
                         PC1   PC2   PC3   PC4
Explained variance     2.933 0.907 0.133 0.027
Standard deviations    1.712 0.952 0.365 0.166
Proportion of variance 0.733 0.227 0.033 0.007
Cumulative proportion  0.733 0.960 0.993 1.000
> print(iris.rpca) # Prints the rotations
Standard deviations:
[1] 1.712 0.952 0.365 0.166

Eigenvalues:
[1] 2.933 0.907 0.133 0.027

Rotation:
                PC1    PC2    PC3    PC4
Sepal.Length  0.504 -0.455  0.709  0.191
Sepal.Width  -0.302 -0.889 -0.331 -0.091
Petal.Length  0.577 -0.034 -0.219 -0.786
Petal.Width   0.567 -0.035 -0.583  0.580
> plot(iris.rpca) # Produce screeplot, variable and individuls factor maps.
Error: The package 'ggplot2' is needed for this function to work. Please install it.
Execution halted
Running examples in ‘rsvg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rsvg
> ### Title: Render SVG into Bitmap
> ### Aliases: rsvg rsvg_pdf rsvg_png rsvg_ps rsvg_raw rsvg_svg rsvg_webp
> 
> ### ** Examples
> 
> # create some svg
> options(example.ask=FALSE)
> tmp <- tempfile()
> svglite::svglite(tmp, width = 10, height = 7)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = factor(cyl))
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’ ‘purrr’
Error in re-building vignettes:
  ...
Loading required package: rtdists
Loading required package: dplyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'dplyr'
Loading required package: tidyr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'tidyr'
Loading required package: purrr
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'purrr'
Loading required package: lattice
Loading required package: latticeExtra
Loading required package: RColorBrewer
Loading required package: binom
Quitting from lines 29-52 (reanalysis_rr98.Rmd) 
Error: processing vignette ‘reanalysis_rr98.Rmd’ failed with diagnostics:
could not find function "%>%"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘rtf.Rnw’ failed with diagnostics:
 chunk 29 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘rbokeh’ ‘tibble’ ‘tidyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  bitmap.c:1594:29: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/Rttf2pt1.Rcheck/00install.out’ for details.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘DT’ ‘ggthemes’ ‘plotly’ ‘colourpicker’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘readr’ ‘tibble’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘keyholder’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘choroplethr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggforce’ ‘ggplot2’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘bang’ ‘revdbayes’
Unavailable namespace imported from by a ':::' call: ‘revdbayes’
  See the note in ?`:::` about the use of this operator.
Packages required but not available: ‘keras’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘colourpicker’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘FactoMineR’ ‘mixOmics’

Package suggested but not available for checking: ‘emmeans’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘Morpho’ ‘rgl’
Running examples in ‘Rvcg-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: checkFaceOrientation
> ### Title: check the orientation of a mesh
> ### Aliases: checkFaceOrientation
> 
> ### ** Examples
> 
> data(dummyhead)
> ## now we invert faces inwards
> checkFaceOrientation(dummyhead.mesh)
[1] TRUE
> dummyinward <- Morpho::invertFaces(dummyhead.mesh)
Error in loadNamespace(name) : there is no package called ‘Morpho’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘ggraph’
Running examples in ‘rvinecopulib-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.vinecop_dist
> ### Title: Plotting 'vinecop_dist' and 'vinecop' objects.
> ### Aliases: plot.vinecop_dist contour.vinecop_dist plot.vinecop
> ###   contour.vinecop plot.vinecop contour.vinecop_dist contour.vinecop
> ### Keywords: plot
> 
> ### ** Examples
> 
> # set up vine copula model
> d <- 20
> n <- 2e2
> u <- matrix(runif(n*d), n, d)
> vc <- vinecop(u, "indep")
> 
> # plot
> plot(vc, tree = c(1,2))
Error in plot.vinecop(vc, tree = c(1, 2)) : 
  The 'ggraph' package must be installed to plot.
Calls: plot -> plot.vinecop
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rvinecopulib)
  > 
  > test_check("rvinecopulib")
  ── 1. Error: plot functions work (@test_vinecop_dist.R#73)  ────────────────────
  The 'ggraph' package must be installed to plot.
  1: expect_silent(p <- plot(vc, edge_labels = "family", var_names = "legend")) at testthat/test_vinecop_dist.R:73
  2: quasi_capture(enquo(object), evaluate_promise)
  3: capture(act$val <- eval_bare(get_expr(quo), get_env(quo)))
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: plot(vc, edge_labels = "family", var_names = "legend")
  10: plot.vinecop_dist(vc, edge_labels = "family", var_names = "legend")
  11: stop("The 'ggraph' package must be installed to plot.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 172 SKIPPED: 0 FAILED: 1
  1. Error: plot functions work (@test_vinecop_dist.R#73) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘tibble’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘viridis’ ‘ggdendro’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘tibble’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 76-79 (RxODE-data-frame.Rmd) 
Error: processing vignette ‘RxODE-data-frame.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Package required but not available: ‘biclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tidyr’ ‘dplyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <setup>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'ggplot2'
Loading required package: grid
Warning in block_exec(params) :
  failed to tidy R code in chunk <sumchisqpow>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Loading required package: polynom
Quitting from lines 409-415 (sadists.Rnw) 
Error: processing vignette ‘sadists.Rnw’ failed with diagnostics:
could not find function "qplot"
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘saeSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: mvtnorm

Error: processing vignette ‘sc-intro.Rnw’ failed with diagnostics:
 chunk 1 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Execution halted
Packages suggested but not available for checking: ‘car’ ‘ggplot2’ ‘mixer’
Errors in running code in vignettes:
when running code in ‘sandwich-OOP.Rnw’
  ...

> library("AER")

  When sourcing ‘sandwich-OOP.R’:
Error: there is no package called ‘AER’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric


Attaching package: ‘pcse’

The following object is masked from ‘package:sandwich’:

    vcovPC

Loading required package: Formula
Classes and Methods for R developed in the
Political Science Computational Laboratory
Department of Political Science
Stanford University
Simon Jackman
hurdle and zeroinfl functions by Achim Zeileis
Warning in packageDescription("lme4") : no package 'lme4' was found
Error: processing vignette ‘sandwich-CL.Rnw’ failed with diagnostics:
at sandwich-CL.Rnw:1304, $ operator is invalid for atomic vectors
Execution halted
Packages required but not available: ‘tibble’ ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘purrr’ ‘readr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sbgcop-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sbgcop.mcmc
> ### Title: Semiparametric Bayesian Gaussian copula estimation and
> ###   imputation
> ### Aliases: sbgcop.mcmc plot.psgc summary.psgc print.sum.psgc
> ### Keywords: multivariate models
> 
> ### ** Examples
> 
> fit<-sbgcop.mcmc(swiss)
10 percent done  Wed May 23 06:39:28 2018 
20 percent done  Wed May 23 06:39:28 2018 
30 percent done  Wed May 23 06:39:29 2018 
40 percent done  Wed May 23 06:39:29 2018 
50 percent done  Wed May 23 06:39:29 2018 
60 percent done  Wed May 23 06:39:29 2018 
70 percent done  Wed May 23 06:39:29 2018 
80 percent done  Wed May 23 06:39:29 2018 
90 percent done  Wed May 23 06:39:29 2018 
100 percent done  Wed May 23 06:39:30 2018 
> summary(fit)
         Length Class  Mode   
C.psamp  3600   -none- numeric
Y.pmean   282   -none- numeric
Y.impute    0   -none- NULL   
LPC       100   -none- numeric
> plot(fit)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Packages required but not available:
  ‘factoextra’ ‘FactoMineR’ ‘ggplot2’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘ggstance’ ‘ggridges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggforce’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: nlme
Quitting from lines 147-161 (Estimating-effect-sizes.Rmd) 
Error: processing vignette ‘Estimating-effect-sizes.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘readODS’ ‘haven’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘ez’
Package required but not available: ‘readr’

Packages suggested but not available for checking: ‘ggetho’ ‘zeitgebr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

The following object is masked from ‘package:graphics’:

    dotchart


Error: processing vignette ‘SDaA_using_survey.Rnw’ failed with diagnostics:
 chunk 24 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘car’ ‘ggplot2’ ‘haven’ ‘DT’ ‘VIM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘SDEFSR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotRules
> ### Title: Plot a rule set generated by a SDEFSR algorithm
> ### Aliases: plotRules
> 
> ### ** Examples
> 
> plotRules(habermanRules)
Package 'ggplot2' is not installed and must be installed to show the rule set plot. Do you want to install it? (Y/n): 
Error in plotRules(habermanRules) : Package ggplot2 is not available
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 538-540 (SDEFSRpackage.Rmd) 
Error: processing vignette ‘SDEFSRpackage.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggmap’ ‘ggsn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sdmpredictors-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_correlation
> ### Title: Plot the correlation matrix for the provided layercodes
> ### Aliases: plot_correlation
> 
> ### ** Examples
> 
> correlation <- layers_correlation(c("BO_calcite", "BO_damin", "MS_bathy_5m"))
> p <- plot_correlation(correlation)
Error: ggplot2 needed for the 'plot_correlation' function to work. Please install it.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: raster
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.2-20, (SVN revision 725)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.4, released 2018/03/19
 Path to GDAL shared files: /usr/share/gdal/2.2
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 5.0.1, April 1st, 2018, [PJ_VERSION: 501]
 Path to PROJ.4 shared files: (autodetected)
 Linking to sp version: 1.2-7 
trying URL ‘http://sdmpredictors.samuelbosch.com/BO_ph_lonlat.tif’
Content type 'image/tiff' length 2518560 bytes (2.4 MB)
==================================================
downloaded 2.4 MB

trying URL ‘http://sdmpredictors.samuelbosch.com/BO_salinity_lonlat.tif’
Content type 'image/tiff' length 5841760 bytes (5.6 MB)
==================================================
downloaded 5.6 MB

trying URL ‘http://sdmpredictors.samuelbosch.com/BO_ph.tif’
Content type 'image/tiff' length 3201193 bytes (3.1 MB)
==================================================
downloaded 3.1 MB

Quitting from lines 136-163 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
ggplot2 needed for the 'plot_correlation' function to work. Please install it.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
[1] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio1.bil" 
[2] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio11.bil"
[3] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio12.bil"
[4] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio14.bil"
[5] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio16.bil"
[6] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio5.bil" 
[7] "/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/sdmvspecies/external/env/bio7.bil" 

Error: processing vignette ‘sdmvspecies.Rnw’ failed with diagnostics:
 chunk 3 (label = bell_shaped_response_function) 
Error in library("ggplot2") : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘spsurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘styler’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘waterData’
Packages suggested but not available for checking: ‘spsurvey’ ‘readxl’
Error in re-building vignettes:
  ...
This is secr 3.1.6. For overview type ?secr
No errors found :-)
Quitting from lines 246-249 (secr-datainput.Rmd) 
Error: processing vignette ‘secr-datainput.Rmd’ failed with diagnostics:
package readxl is required for input from Excel spreadsheets
Execution halted
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘rgl’ ‘demography’ ‘tibble’ ‘labelled’ ‘forcats’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘rgl’
Packages required but not available: ‘dplyr’ ‘ggplot2’

Packages suggested but not available for checking: ‘leaflet’ ‘moveHMM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘factoextra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘shiny.semantic’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘qdap’ ‘NetworkToolbox’ ‘ggplot2’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘qgraph’ ‘rockchalk’

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggExtra’ ‘rgl’
Packages required but not available:
  ‘doBy’ ‘FactoMineR’ ‘factoextra’ ‘ggdendro’ ‘plotly’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘doBy’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘lexicon’ ‘syuzhet’ ‘textclean’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘quanteda’ ‘caret’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘qvalue’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘dbplyr’ ‘readr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dendextend’

Packages suggested but not available for checking: ‘biclust’ ‘DendSer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
trying URL ‘https://pure.strath.ac.uk/portal/files/43595106/Figure_2.zip’
downloaded 270 KB

Quitting from lines 45-52 (Introduction.Rmd) 
Error: processing vignette ‘Introduction.Rmd’ failed with diagnostics:
there is no package called 'hyperSpec'
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘caret’ ‘dplyr’ ‘plotly’ ‘Hmisc’ ‘tidyr’
  ‘ggridges’

Packages suggested but not available for checking: ‘loomR’ ‘MAST’ ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘tmap’ ‘tibble’ ‘dplyr’ ‘tidyr’ ‘tidyselect’ ‘ggplot2’ ‘mapview’
Running ‘aggregate.R’ [1s/2s]
  Comparing ‘aggregate.Rout’ to ‘aggregate.Rout.save’ ...4c4
< Linking to GEOS 3.6.2, GDAL 2.2.4, proj.4 5.0.1
---
> Linking to GEOS 3.6.2, GDAL 2.2.3, proj.4 4.9.3
  Running ‘cast.R’ [1s/2s]
  Comparing ‘cast.Rout’ to ‘cast.Rout.save’ ... OK
  Running ‘crs.R’ [1s/1s]
  Comparing ‘crs.Rout’ to ‘crs.Rout.save’ ... OK
  Running ‘dist.R’ [1s/2s]
  Comparing ‘dist.Rout’ to ‘dist.Rout.save’ ... OK
  Running ‘dplyr.R’ [1s/1s]
Running the tests in ‘tests/dplyr.R’ failed.
Complete output:
  > suppressPackageStartupMessages(library(sf))
  > library(dplyr)
  Error in library(dplyr) : there is no package called 'dplyr'
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 461-462 (sf1.Rmd) 
Error: processing vignette ‘sf1.Rmd’ failed with diagnostics:
package tibble not available: install first?
Execution halted
Package required but not available: ‘tensorflow’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘SGP’
Error in re-building vignettes:
  ...
Quitting from lines 2-11 (SGPdata.Rmd) 
Error: processing vignette ‘SGPdata.Rmd’ failed with diagnostics:
there is no package called 'toOrdinal'
Execution halted
Package suggested but not available for checking: ‘threejs’
Packages required but not available: ‘aqp’ ‘soilDB’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘alakazam’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘ggExtra’

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘shinyaframe-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: aDataScene
> ### Title: A-Frame Scene with R data
> ### Aliases: aDataScene
> 
> ### ** Examples
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Package suggested but not available for checking: ‘colourpicker’
Package suggested but not available for checking: ‘styler’
Packages required but not available:
  ‘heatmaply’ ‘dplyr’ ‘viridis’ ‘plotly’ ‘readxl’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘difNLR’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘highcharter’
Running examples in ‘shinyjqui-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Interactions
> ### Title: Mouse interactions
> ### Aliases: Interactions jqui_resizabled jqui_sortabled jqui_draggabled
> ###   jqui_droppabled jqui_selectabled jqui_sortable jqui_draggable
> ###   jqui_droppable jqui_selectable jqui_resizable
> 
> ### ** Examples
> 
> library(shiny)
> library(highcharter)
Error in library(highcharter) : there is no package called ‘highcharter’
Execution halted
Package required but not available: ‘purrr’

Packages suggested but not available for checking: ‘dplyr’ ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bayesplot’ ‘colourpicker’ ‘DT’ ‘ggplot2’ ‘rstan’ ‘threejs’

Package suggested but not available for checking: ‘rstanarm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘readr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘hdrcde’

Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘hdrcde’ ‘viridis’ ‘tidyr’ ‘dplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Packages suggested but not available for checking: ‘cowplot’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 42-50 (sigmoid.Rmd) 
Error: processing vignette ‘sigmoid.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘phylobase’ ‘phyext2’ ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘SimMultiCorrData’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘robCompositions’
Error in re-building vignettes:
  ...
Loading required package: Rcpp
Loading required package: lattice
Loading required package: parallel
Loading required package: boot

Attaching package: ‘boot’

The following object is masked from ‘package:lattice’:

    melanoma

Loading required package: MASS

Error: processing vignette ‘simFrame-intro.Rnw’ failed with diagnostics:
 chunk 23 
Error in library("robCompositions") : 
  there is no package called ‘robCompositions’
Execution halted
Packages required but not available: ‘ggplot2’ ‘DiagrammeR’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘simmer.plot’ ‘dplyr’ ‘tidyr’
Packages required but not available: ‘VIM’ ‘EnvStats’

Package suggested but not available for checking: ‘haven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘VIM’
Packages required but not available:
  ‘SimMultiCorrData’ ‘SimCorrMix’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘moveHMM’
Package required but not available: ‘car’

Package suggested but not available for checking: ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘simstudy-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: addCondition
> ### Title: Add a single column to existing data set based on a condition
> ### Aliases: addCondition
> 
> ### ** Examples
> 
> 
> # New data set
> 
> def <- defData(varname = "x", dist = "categorical", formula = ".33;.33")
> def <- defData(def, varname="y", dist="uniform", formula="-5;5")
> 
> dt <- genData(1000, def)
> 
> # Define conditions
> 
> defC <- defCondition(condition = "x == 1", formula = "5 + 2*y-.5*y^2",
+                      variance = 1,dist = "normal")
> defC <- defCondition(defC, condition = "x == 2",
+                      formula = "3 - 3*y + y^2", variance = 2, dist="normal")
> defC <- defCondition(defC, condition = "x == 3",
+                      formula = "abs(y)", dist="poisson")
> 
> # Add column
> 
> dt <- addCondition(defC, dt, "NewVar")
> 
> # Plot data
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: data.table
Quitting from lines 38-282 (simstudy.Rmd) 
Error: processing vignette ‘simstudy.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

Packages suggested but not available for checking: ‘ggplot2’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [37s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Got this Sys.setenv line from https://github.com/luckyrandom/cmaker/blob/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0/tests/testthat.R
  > # so that devtools:check() won't hang.
  > # setting R_TESTS to empty string because of
  > # https://github.com/hadley/testthat/issues/144
  > # revert this when that issue in R is fixed.
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(simulator)
  
  Attaching package: 'simulator'
  
  The following object is masked from 'package:testthat':
  
      describe
  
  > 
  > test_check("simulator")
  ── 1. Failure: create makes a template that can be run without error (@test-crea
  any(grepl("error", readLines(a), ignore.case = TRUE)) isn't false.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 3 FAILED: 1
  1. Failure: create makes a template that can be run without error (@test-create.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 130-154 (uniform_rng_with_sitmo.Rmd) 
Error: processing vignette ‘uniform_rng_with_sitmo.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘haven’ ‘purrr’ ‘tibble’ ‘tidyselect’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘Hmisc’ ‘sjmisc’ ‘sjPlot’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘haven’ ‘purrr’ ‘sjlabelled’ ‘tibble’ ‘tidyr’
  ‘tidyselect’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘sjPlot’ ‘sjstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘forcats’ ‘ggeffects’ ‘ggplot2’ ‘merTools’ ‘modelr’
  ‘purrr’ ‘sjlabelled’ ‘sjmisc’ ‘sjstats’ ‘tidyselect’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘car’ ‘ggrepel’ ‘ggridges’ ‘lmerTest’ ‘rstanarm’ ‘viridis’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bayesplot’ ‘broom’ ‘dplyr’ ‘emmeans’ ‘modelr’ ‘purrr’ ‘sjlabelled’
  ‘sjmisc’ ‘tidyr’ ‘tidyselect’ ‘tibble’

Packages suggested but not available for checking:
  ‘AER’ ‘apaTables’ ‘brms’ ‘car’ ‘ggplot2’ ‘pROC’ ‘sjPlot’ ‘rstan’
  ‘rstanarm’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘hierfstat’ ‘pegas’ ‘rmetasim’ ‘strataG’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggrepel’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘agricolae’ ‘car’ ‘mosaic’
Error in re-building vignettes:
  ...
Loading required package: mosaic
Loading required package: Sleuth2
Quitting from lines 130-145 (chapter01-HortonMosaic.Rnw) 
Error: processing vignette ‘chapter01-HortonMosaic.Rnw’ failed with diagnostics:
could not find function "trellis.par.set"
Execution halted
Packages suggested but not available for checking:
  ‘Hmisc’ ‘agricolae’ ‘car’ ‘mosaic’
Error in re-building vignettes:
  ...
Loading required package: mosaic
Loading required package: Sleuth3
Quitting from lines 130-145 (chapter01-HortonMosaic.Rnw) 
Error: processing vignette ‘chapter01-HortonMosaic.Rnw’ failed with diagnostics:
could not find function "trellis.par.set"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 65-69 (slim.Rmd) 
Error: processing vignette ‘slim.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘Hmisc’ ‘weights’ ‘candisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rgl’

Package suggested but not available for checking: ‘demography’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘greybox’ ‘forecast’

Package suggested but not available for checking: ‘Mcomp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘imager’ ‘ggplot2’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Packages suggested but not available for checking: ‘tibble’ ‘purrrlyr’
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tibble")
  Error in library("tibble") : there is no package called 'tibble'
  Execution halted
Packages required but not available: ‘car’ ‘ggplot2’ ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘oai’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘aqp’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘aqp’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘GSIF’

Package suggested but not available for checking: ‘plotKML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘tdr’
Package required but not available: ‘dplyr’

Package suggested but not available for checking: ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Sotkanet R tools (C) 2013-2017 rOpenGov
https://github.com/ropengov/sotkanet
Retrieving indicator 10013
Quitting from lines 99-114 (tutorial.Rmd) 
Error: processing vignette ‘tutorial.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggplot2’ ‘r2cytoscape’
Running examples in ‘SourceSet-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: easyLookSource
> ### Title: Easy look results
> ### Aliases: easyLookSource
> 
> ### ** Examples
> 
> ## Load the SourceSetObj obtained from the source set analysis of ALL dataset
> 
> # see vignette for more details
> print(load(file=system.file("extdata","ALLsourceresult.RData",package = "SourceSet")))
[1] "results.all"
> class(results.all)
[1] "sourceSetList"
> n.primary<-length(lapply(results.all,function(x) x$primarySet))
> 
> # show only genes that appear in at least one of the source sets of the investigated pathways
> easyLookSource(sourceObj=results.all, maxnum.variable = n.primary,
+                label.variable = "Genes",label.graph = "Pathways")
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: easyLookSource ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Identifing all possible orderings..
Total run time: 1.34 secs
Quitting from lines 311-312 (SourceSet.Rmd) 
Error: processing vignette ‘SourceSet.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘SpaDES.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘quickPlot’ ‘DiagrammeR’ ‘dplyr’

Package suggested but not available for checking: ‘SpaDES.tools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘quickPlot’ ‘SpaDES.addins’ ‘SpaDES.core’ ‘SpaDES.tools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘quickPlot’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘earlywarnings’
Package suggested but not available for checking: ‘Infusion’
Packages required but not available: ‘sparklyr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘dbplyr’ ‘readr’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘nycflights13’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sparklyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘RGraphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 1270-1273 (sparseHessianFD.Rnw) 
Error: processing vignette ‘sparseHessianFD.Rnw’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 73-87 (sparseMVN.Rnw) 
Error: processing vignette ‘sparseMVN.Rnw’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Found the following significant warnings:
  sparseSVM.c:367:30: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/sparseSVM.Rcheck/00install.out’ for details.
Packages required but not available: ‘readr’ ‘rms’ ‘EnvStats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘leaflet’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘plot3Drgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘broom’ ‘ggpolypath’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘spbabel’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘imager’ ‘tidyverse’ ‘rgl’
Packages required but not available:
  ‘hyperSpec’ ‘rgl’ ‘GGally’ ‘ggplot2’ ‘ggdendro’ ‘caret’ ‘qdap’ ‘xcms’
  ‘MAIT’ ‘speaq’

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Rssa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggmap’ ‘ggplot2’
Running examples in ‘spew-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_pop_totals
> ### Title: Plot characteristic summary output from
> ###   summarize_top_spew_region as totals
> ### Aliases: plot_pop_totals
> 
> ### ** Examples
> 
> data(tartanville)
> 
> tartanville_syneco <- spew(tartanville$pop_table, tartanville$shapefile, 
+                            tartanville$pums_h, tartanville$pums_p)
Loading required package: sp
[1] "Place has 0 Households!"
> plot_syneco(tartanville, tartanville_syneco, region_name = "Tartanville")
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Calls: plot_syneco ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘testthat.R’ [22s/28s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(spew)
  > 
  > test_check("spew")
  ── 1. Error: functions for summarizing spew synecos in console (@test-summarize-
  there is no package called 'ggplot2'
  1: ggplot2::fortify at testthat/test-summarize-spew.R:6
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 100 SKIPPED: 7 FAILED: 1
  1. Error: functions for summarizing spew synecos in console (@test-summarize-spew.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette ‘spew-quickstart.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘quadmesh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ezsim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘mlr’ ‘ggplot2’

Package suggested but not available for checking: ‘caret’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mvmesh’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  timeFuns.c:1084:34: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/splusTimeDate.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘antaresViz’
Package required but not available: ‘biomod2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘rgbif’ ‘rbison’ ‘rebird’ ‘rvertnet’ ‘tibble’

Package suggested but not available for checking: ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  wdl.cpp:184:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following apparent S3 methods exported but not registered:
  points.within
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'points.within':
  ‘points.within’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package required but not available: ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Packages suggested but not available for checking: ‘dplyr’ ‘GGally’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘autothresholdr’ ‘viridis’ ‘ggplot2’ ‘imager’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘dbplyr’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ssc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coBC
> ### Title: CoBC method
> ### Aliases: coBC
> 
> ### ** Examples
> 
> 
> library(ssc)
> 
> ## Load Wine data set
> data(wine)
> 
> cls <- which(colnames(wine) == "Wine")
> x <- wine[, -cls] # instances without classes
> y <- wine[, cls] # the classes
> x <- scale(x) # scale the attributes
> 
> ## Prepare data
> set.seed(20)
> # Use 50% of instances for training
> tra.idx <- sample(x = length(y), size = ceiling(length(y) * 0.5))
> xtrain <- x[tra.idx,] # training instances
> ytrain <- y[tra.idx]  # classes of training instances
> # Use 70% of train instances as unlabeled set
> tra.na.idx <- sample(x = length(tra.idx), size = ceiling(length(tra.idx) * 0.7))
> ytrain[tra.na.idx] <- NA # remove class information of unlabeled instances
> 
> # Use the other 50% of instances for inductive testing
> tst.idx <- setdiff(1:length(y), tra.idx)
> xitest <- x[tst.idx,] # testing instances
> yitest <- y[tst.idx] # classes of testing instances
> 
> ## Example: Training from a set of instances with 1-NN as base classifier.
> set.seed(1)
> m1 <- coBC(x = xtrain, y = ytrain, 
+            learner = caret::knn3, 
+            learner.pars = list(k = 1),
+            pred = "predict")
Error in loadNamespace(name) : there is no package called ‘caret’
Calls: coBC ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘caret’ ‘klaR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘sampleSelection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘ggfortify’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘Hmisc’ ‘dplyr’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pegas’ ‘adegenet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘afex’ ‘lmerTest’
Error in re-building vignettes:
  ...
Quitting from lines 362-367 (using-standardize.Rmd) 
Error: processing vignette ‘using-standardize.Rmd’ failed with diagnostics:
there is no package called 'afex'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘eemR’ ‘readr’ ‘tibble’ ‘plotly’ ‘GGally’
  ‘drc’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages which this enhances but not available for checking:
  ‘AER’ ‘dynlm’ ‘erer’ ‘rms’ ‘sampleSelection’ ‘Zelig’
Packages required but not available:
  ‘readr’ ‘tidyr’ ‘purrr’ ‘ggplot2’ ‘ggdendro’ ‘ggrepel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking: ‘tidyverse’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: proxy

Attaching package: ‘proxy’

The following objects are masked from ‘package:stats’:

    as.dist, dist

The following object is masked from ‘package:base’:

    as.matrix

Loading required package: clue
Loading required package: survey
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: ‘survey’

The following object is masked from ‘package:graphics’:

    dotchart

Loading required package: RANN
Loading required package: lpSolve
Loading required package: Hmisc

Error: processing vignette ‘Statistical_Matching_with_StatMatch.Rnw’ failed with diagnostics:
 chunk 4 
Error in spearman2(n.income ~ area5 + urb + hsize + age + sex + marital +  : 
  could not find function "spearman2"
Execution halted
Package suggested but not available for checking: ‘EpiModel’
Package required but not available: ‘tidytext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘broom’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘stm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘stm’ ‘tidygraph’ ‘ggraph’ ‘ggrepel’ ‘ggplot2’ ‘purrr’ ‘dplyr’
  ‘tibble’

Package suggested but not available for checking: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘demography’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking:
  ‘ggmap’ ‘tigris’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘UsingR’
Packages required but not available: ‘readr’ ‘dplyr’

Package which this enhances but not available for checking: ‘tmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’

Packages suggested but not available for checking: ‘dtplyr’ ‘mvoutlier’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘apex’ ‘adegenet’ ‘DT’ ‘ggplot2’ ‘Hmisc’ ‘pegas’ ‘swfscMisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ndjson’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Building shared library for Rcpp code chunk...
Quitting from lines 60-85 (strider.Rmd) 
Error: processing vignette ‘strider.Rmd’ failed with diagnostics:
Package 'BH' referenced from Rcpp::depends in source file file308b49e464aa.cpp is not available.
Execution halted
Packages required but not available:
  ‘broom’ ‘car’ ‘ggplot2’ ‘lmerTest’ ‘phia’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘rgl’

Package suggested but not available for checking: ‘demography’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘car’ ‘dynlm’
Error in re-building vignettes:
  ...
Loading required package: StructFDR
Loading required package: nlme
Loading required package: ape
Loading required package: cluster
Loading required package: dirmult
Loading required package: matrixStats
Loading required package: ggplot2
Loading required package: reshape
Quitting from lines 172-187 (StructFDR.Rmd) 
Error: processing vignette ‘StructFDR.Rmd’ failed with diagnostics:
could not find function "ggplot"
Execution halted
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘rematch2’ ‘tibble’

Packages suggested but not available for checking: ‘data.tree’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggvis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘readr’ ‘tidyr’ ‘purrr’ ‘dplyr’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘d3r’ ‘dplyr’

Package suggested but not available for checking: ‘tidyr’

Package which this enhances but not available for checking: ‘treemap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘ggdendro’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘bartMachine’ ‘caret’ ‘ggplot2’
Error in re-building vignettes:
  ...
Quitting from lines 191-213 (Guide-to-SuperLearner.Rmd) 
Error: processing vignette ‘Guide-to-SuperLearner.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘ggformula’ ‘mosaic’
Package required but not available: ‘prim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rgl’ ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘survAUC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: schemper
> ### Title: Distance-based estimator of survival predictive accuracy
> ###   proposed by Schemper and Henderson
> ### Aliases: schemper
> ### Keywords: classif
> 
> ### ** Examples
> 
> 
> library(rms)
Error in library(rms) : there is no package called ‘rms’
Execution halted
Packages suggested but not available for checking:
  ‘rmapshaper’ ‘INLA’ ‘ggplot2’
Packages required but not available: ‘rms’ ‘rstan’

Packages suggested but not available for checking: ‘shinystan’ ‘INLA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘cowplot’ ‘ggthemes’ ‘viridis’

Packages suggested but not available for checking: ‘broom’ ‘readr’ ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggpubr’ ‘broom’ ‘dplyr’ ‘tidyr’ ‘survMisc’ ‘purrr’
  ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggsci’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘broom’

Package suggested but not available for checking: ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘robets’ ‘forecastHybrid’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘tsDyn’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘forecast’ ‘tibble’ ‘tidyr’ ‘timetk’

Packages suggested but not available for checking:
  ‘forcats’ ‘purrr’ ‘readr’ ‘robets’ ‘tidyquant’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘SWMPr’ ‘broom’ ‘dplyr’ ‘EnvStats’ ‘ggplot2’ ‘ggthemes’ ‘leaflet’
  ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘ggmap’ ‘dplyr’ ‘openair’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘clusterSim’ ‘rgl’ ‘shapes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mpoly’
Running examples in ‘symmoments-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: convert.mpoly
> ### Title: Convert between mpoly and list representations of multivariate
> ###   polynomials
> ### Aliases: ' convert.mpoly '
> 
> ### ** Examples
> 
> # create an mpoly object here
> 
> # convert from mpoly to list representation
> library(mpoly)
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: cubature
Loading required package: combinat

Attaching package: ‘combinat’

The following object is masked from ‘package:utils’:

    combn

Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

The following object is masked from ‘package:stats’:

    deriv

The following object is masked from ‘package:base’:

    single


Error: processing vignette ‘symmoments.rnw’ failed with diagnostics:
 chunk 13 (label = noncentral3a) 
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’

Package suggested but not available for checking: ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘lmerTest’ ‘labelled’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘corrgram’ ‘car’
Package required but not available: ‘Hmisc’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘tabplot-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: num2fac
> ### Title: Transform a numerical vector to a factor
> ### Aliases: num2fac
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(diamonds)
Warning in data(diamonds) : data set ‘diamonds’ not found
> 
> diamonds$price2 <- num2fac(diamonds$price)
Loading required namespace: classInt
Error in quantile(num, na.rm = TRUE) : object 'diamonds' not found
Calls: num2fac -> quantile
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 19-24 (tabplot-timings.Rmd) 
Error: processing vignette ‘tabplot-timings.Rmd’ failed with diagnostics:
object ‘diamonds’ not found
Execution halted
Packages required but not available: ‘dplyr’ ‘purrr’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘spex’ ‘spbabel’ ‘tibble’ ‘viridis’ ‘gibble’

Package suggested but not available for checking: ‘spdplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 100-103 (new-methods.Rmd) 
Error: processing vignette ‘new-methods.Rmd’ failed with diagnostics:
there is no package called 'forecast'
Execution halted
Packages required but not available:
  ‘broom’ ‘pixiedust’ ‘car’ ‘ggplot2’ ‘viridis’

Package suggested but not available for checking: ‘cowplot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pmatch’
Package suggested but not available for checking: ‘LSAmitR’
Packages suggested but not available for checking: ‘rms’ ‘Hmisc’
Error in re-building vignettes:
  ...
Quitting from lines 13-18 (fda-example.Rmd) 
Error: processing vignette ‘fda-example.Rmd’ failed with diagnostics:
there is no package called 'Hmisc'
Execution halted
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘kableExtra’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘tibble’

Packages suggested but not available for checking: ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’ ‘tidyr’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘bold’ ‘ritis’ ‘tibble’ ‘worrms’ ‘natserv’ ‘wikitaxa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘tcgsaseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘DESeq2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Mcomp’ ‘forecast’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘SPOT’ ‘adabag’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘DT’ ‘leaflet’ ‘threejs’ ‘d3heatmap’ ‘tidyr’ ‘plotly’
  ‘DiagrammeR’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rgl’ ‘ggplot2’ ‘R2wd’
Packages suggested but not available for checking:
  ‘Lahman’ ‘dplyr’ ‘ggplot2’
Package required but not available: ‘eva’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘arulesViz’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tsBSS’ ‘ICtest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tfruns’

Packages suggested but not available for checking: ‘keras’ ‘tfestimators’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 29-51 (GIAValidationExample.Rmd) 
Error: processing vignette ‘GIAValidationExample.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Package required but not available: ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘tidyr’ ‘FactoMineR’ ‘tibble’ ‘ggrepel’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘GGally’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘btergm’ ‘Zelig’

Packages which this enhances but not available for checking:
  ‘AER’ ‘dynlm’ ‘erer’ ‘rms’ ‘sampleSelection’ ‘systemfit’ ‘xergm’
Package required but not available: ‘lexicon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘textreuse’
Running examples in ‘textrank-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: textrank_candidates_lsh
> ### Title: Use locality-sensitive hashing to get combinations of sentences
> ###   which contain words which are in the same minhash bucket
> ### Aliases: textrank_candidates_lsh
> 
> ### ** Examples
> 
> library(textreuse)
Error in library(textreuse) : there is no package called ‘textreuse’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 140-149 (textrank.Rmd) 
Error: processing vignette ‘textrank.Rmd’ failed with diagnostics:
there is no package called 'textreuse'
Execution halted
Packages required but not available:
  ‘dplyr’ ‘lexicon’ ‘quanteda’ ‘textclean’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tensorflow’ ‘tidyselect’

Packages suggested but not available for checking: ‘tfestimators’ ‘keras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tensorflow’ ‘tfruns’ ‘tidyselect’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘ggplot2’ ‘modelr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘plotly’ ‘rstan’ ‘stm’

Package suggested but not available for checking: ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘phyloseq’ ‘tidyverse’ ‘tidyr’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘forecast’ ‘hts’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘dplyr’ ‘nycflights13’
Installation failed.
See ‘/home/hornik/tmp/R.check/r-devel-gcc/Work/PKGS/tibble.Rcheck/00install.out’ for details.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’

Packages suggested but not available for checking:
  ‘broom’ ‘gapminder’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘modelr’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tigris’ ‘purrr’ ‘tidyr’ ‘readr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tidyr’ ‘fuzzyjoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘dplyr’ ‘tidyr’

Packages suggested but not available for checking: ‘data.tree’ ‘seriation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dbplyr’ ‘dplyr’ ‘readr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tibble’ ‘tidyselect’ ‘tidyverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘forcats’ ‘ggplot2’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘MplusAutomation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘broom’ ‘rsample’ ‘tidyr’ ‘dplyr’ ‘rstanarm’ ‘purrr’
  ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking: ‘dbplyr’ ‘nycflights13’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyverse’ ‘dplyr’ ‘ggplot2’ ‘purrr’ ‘tibble’ ‘tidyr’ ‘timetk’

Packages suggested but not available for checking:
  ‘alphavantager’ ‘broom’ ‘tibbletime’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘purrr’ ‘tibble’ ‘tidyselect’

Package suggested but not available for checking: ‘gapminder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tibble’ ‘readr’ ‘tidyr’ ‘dplyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘broom’ ‘purrr’

Packages suggested but not available for checking:
  ‘readr’ ‘tidyr’ ‘quanteda’ ‘ggplot2’ ‘gutenbergr’ ‘stm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘ggtree’ ‘treeio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘dbplyr’ ‘forcats’ ‘ggplot2’ ‘haven’ ‘modelr’ ‘purrr’
  ‘readr’ ‘readxl’ ‘tibble’ ‘tidyr’

Package suggested but not available for checking: ‘feather’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘readxl’ ‘dplyr’ ‘tidyr’ ‘purrr’ ‘ggplot2’ ‘cellranger’
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyxl)
  > 
  > test_check("tidyxl")
  ── 1. Error: (unknown) (@test-names.R#3)  ──────────────────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-names.R:3
  2: stop(txt, domain = NA)
  
  ── 2. Error: (unknown) (@test-validation.R#3)  ─────────────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-validation.R:3
  2: stop(txt, domain = NA)
  
  ── 3. Error: (unknown) (@test-xlex.R#3)  ───────────────────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-xlex.R:3
  2: stop(txt, domain = NA)
  
  ── 4. Error: (unknown) (@test-xlsx_color_theme.R#3)  ───────────────────────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test-xlsx_color_theme.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 251 SKIPPED: 0 FAILED: 4
  1. Error: (unknown) (@test-names.R#3) 
  2. Error: (unknown) (@test-validation.R#3) 
  3. Error: (unknown) (@test-xlex.R#3) 
  4. Error: (unknown) (@test-xlsx_color_theme.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 34-39 (data-validation-rules.Rmd) 
Error: processing vignette ‘data-validation-rules.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘abd’ ‘mosaic’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘alakazam’ ‘tidyr’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘tightClust-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tight.clust
> ### Title: Tight Clustering
> ### Aliases: tight.clust
> ### Keywords: cluster
> 
> ### ** Examples
> 
> ## load the test dataset
> data(tclust.test.data)
> ## find 10 tight clusters
> ptm<-proc.time()
> ## k.min=25, tighter clusters will be found
> ## target=1 is used to save time, target=10 is recommended
> tclust1<-tight.clust(tclust.test.data$Data, target=1, k.min=25, random.seed=12345)
Number of points: 1100 	Dimension: 75 

Looking for tight cluster 1 ...
k = 25
k = 26
1 tight cluster(s) found!
Cluster size: 43 	Remaining number of points: 1057 

> proc.time()-ptm
   user  system elapsed 
  2.674   0.114   4.444 
> ## plot the heat map of cluster result
> plot(tclust1)
Error in xy.coords(x, y, xlabel, ylabel, log) : 
  'x' is a list, but does not have components 'x' and 'y'
Calls: plot -> plot.default -> xy.coords
Execution halted
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘ggthemes’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘tidyr’ ‘leaflet’
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘mtconnectR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TimeProjection-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plotCalendarHeatmap
> ### Title: Calendar Heatmap
> ### Aliases: plotCalendarHeatmap
> 
> ### ** Examples
> 
> dates = timeSequence(from = '2012-01-01', to = '2012-12-31', by = 'day')
>    plotCalendarHeatmap(as.Date(dates), 1:366)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
Loading required package: plyr

Attaching package: ‘plyr’

The following object is masked from ‘package:lubridate’:

    here

Error in ggplot(tp, aes(monthweek, weekday, fill = values)) : 
  could not find function "ggplot"
Calls: plotCalendarHeatmap
Execution halted
Packages required but not available:
  ‘dplyr’ ‘forecast’ ‘padr’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’

Packages suggested but not available for checking:
  ‘broom’ ‘forcats’ ‘robets’ ‘tidyverse’ ‘tidyquant’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 18-23 (tintHTML.Rmd) 
Error: processing vignette ‘tintHTML.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘broom’ ‘tibble’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘ggplot2’
Package required but not available: ‘Luminescence’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tmaptools’ ‘leaflet’ ‘mapview’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘rmapshaper’

Packages suggested but not available for checking: ‘tmap’ ‘OpenStreetMap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘pca3d’
Error in re-building vignettes:
  ...
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'pca3d'
Quitting from lines 694-697 (tmod.rmd) 
Error: processing vignette ‘tmod.rmd’ failed with diagnostics:
unused argument (group = c("CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "CTRL", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB", "TB"))
Execution halted
Running examples in ‘tm.plugin.dc-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tm_map.DCorpus
> ### Title: Transformations on Distributed Corpora
> ### Aliases: tm_map.DCorpus
> 
> ### ** Examples
> 
> data("crude")
> tm_map(as.DCorpus(crude), content_transformer(tolower))
Warning in file(con, "w") :
  cannot open file '/home/hornik/tmp/scratch/RtmpkDMsbZ/DSL-20180523-065917-gjoxfxyrqb/chunk-242e15dedb3e': No such file or directory
Error in file(con, "w") : cannot open the connection
Calls: tm_map ... DS_write_lines -> <Anonymous> -> <Anonymous> -> file
Execution halted
Packages required but not available: ‘ggplot2’ ‘ggthemes’ ‘ggmap’ ‘GGally’

Package suggested but not available for checking: ‘ggnetwork’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Packages suggested but not available for checking: ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘rmongodb’ ‘ggplot2’
Error in re-building vignettes:
  ...
Loading required package: data.table
tcpl (v1.4.3) loaded with the following settings:
  TCPL_DB:    /home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/tcpl/sql/tcpldb.sqlite
  TCPL_USER:  NA
  TCPL_HOST:  NA
  TCPL_DRVR:  SQLite
Default settings stored in tcpl config file. See ?tcplConf for more information.
toxboot 0.1.1
MongoDB settings (?toxbootConf):
  TOXBOOT_HOST: NA
  TOXBOOT_DBNS: NA
  TOXBOOT_USER: NA
  TOXBOOT_DB: NA
MySQL settings:
  Host: Not Configured
  Database: Not Configured
  User: Not Configured
Loading required package: DBI
Quitting from lines 27-35 (toxboot.Rmd) 
Error: processing vignette ‘toxboot.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘dplyr’ ‘tidyr’ ‘ggplot2’ ‘ggthemes’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package in Depends field not imported from: ‘lgtdl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
ci.plot: no visible global function definition for ‘gaussian’
ci.plot: no visible global function definition for ‘qnorm’
ci.plot: no visible global function definition for ‘plot’
ci.plot: no visible global function definition for ‘lines’
cst.fit.ff: no visible global function definition for ‘pnorm’
cstfit.1: no visible global function definition for ‘var’
gof.test.boots.pf: no visible binding for global variable ‘sd’
gof.test.int.1.ff: no visible global function definition for ‘quantile’
gof.test.int.1.ff: no visible global function definition for ‘var’
gof.test.int.ff: no visible global function definition for ‘pnorm’
gofTest: no visible binding for global variable ‘sd’
plotGof: no visible global function definition for ‘plot’
plotGof : <anonymous>: no visible global function definition for
  ‘lines’
plotGof: no visible global function definition for ‘lines’
sig.test.int.1.ff: no visible global function definition for ‘quantile’
sig.test.int.1.ff: no visible global function definition for ‘var’
sig.test.int.ff: no visible global function definition for ‘pnorm’
test.boots.1: no visible binding for global variable ‘sd’
tpr: no visible global function definition for ‘poisson’
tpr: no visible global function definition for ‘glm.fit’
tpr: no visible global function definition for ‘coef’
tpr: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx coef gaussian glm.fit lines plot pnorm poisson qnorm quantile
  sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "approx", "coef", "gaussian", "glm.fit", "pnorm",
             "poisson", "qnorm", "quantile", "sd", "var")
to your NAMESPACE file.
Rd file 'ci.plot.Rd':
  \usage lines wider than 90 characters:
     ci.plot(x, y, se, level = 0.95, ylim = NULL, newplot = TRUE, fun = gaussian()$linkinv, dfun = gaussian()$mu.eta, ...)

These lines will be truncated in the PDF manual.
File ‘tpr/libs/tpr.so’:
  Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘readxl’ ‘taxize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggmap’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Packages suggested but not available for checking: ‘dplyr’ ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘caret’ ‘dplyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘tibble’ ‘readr’ ‘taxize’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TrajDataMining-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: owMeratniaByCollection
> ### Title: Ow Meratnial By Collection
> ### Aliases: owMeratniaByCollection
> ###   owMeratniaByCollection,TracksCollection,numeric,numeric-method
> 
> ### ** Examples
> 
> 
> library(magrittr)
> 
> library(sp)
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 36-42 (TrajDataMining.Rmd) 
Error: processing vignette ‘TrajDataMining.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages suggested but not available for checking: ‘rgl’ ‘OpenStreetMap’
Error in re-building vignettes:
  ...

Error: processing vignette ‘tracks.Rnw’ failed with diagnostics:
 chunk 1 
Error in library("rgl") : there is no package called ‘rgl’
Execution halted
Packages required but not available: ‘car’ ‘Hmisc’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘trapezoid.Rnw’ failed with diagnostics:
 chunk 2 (label = trapezoid) 
Error in ggplot(data = data.frame(x, density), aes(x = x, y = density)) : 
  could not find function "ggplot"
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette ‘treecm.Rnw’ failed with diagnostics:
 chunk 14 (label = exStabilization5) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘phyloseq’ ‘ggplot2’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ggfittext’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘adegenet’ ‘adephylo’ ‘rgl’ ‘RLumShiny’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘datadr’ ‘ggplot2’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pROC’ ‘rms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘dplyr’

Packages suggested but not available for checking:
  ‘ggplot2’ ‘lplyr’ ‘observer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘ez’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘hdrcde’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 13-16 (quickstart.Rmd) 
Error: processing vignette ‘quickstart.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking:
  ‘dplyr’ ‘tibble’ ‘forecast’ ‘ggplot2’ ‘tsibble’ ‘nycflights13’
Running examples in ‘tsbox-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ts_ts
> ### Title: Convert Everything to Everything
> ### Aliases: ts_ts ts_data.frame ts_ts ts_df ts_ts ts_data.table ts_ts
> ###   ts_dt ts_ts ts_tbl ts_ts ts_timeSeries ts_ts ts_ts ts_tsibble ts_ts
> ###   ts_tslist ts_ts ts_xts ts_ts ts_zoo
> 
> ### ** Examples
> 
> 
> x.ts <- ts_c(mdeaths, fdeaths)
> head(x.ts)
     mdeaths fdeaths
[1,]    2134     901
[2,]    1863     689
[3,]    1877     827
[4,]    1877     677
[5,]    1492     522
[6,]    1249     406
> head(ts_df(x.ts))
       id       time value
1 mdeaths 1974-01-01  2134
2 mdeaths 1974-02-01  1863
3 mdeaths 1974-03-01  1877
4 mdeaths 1974-04-01  1877
5 mdeaths 1974-05-01  1492
6 mdeaths 1974-06-01  1249
> 
> suppressMessages(library(dplyr))
Error in library(dplyr) : there is no package called ‘dplyr’
Calls: suppressMessages -> withCallingHandlers -> library
Execution halted
Packages required but not available: ‘ICtest’ ‘forecast’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘gcmr’
Error in re-building vignettes:
  ...
Loading required package: splines
Loading required package: gamlss.data
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.0-8  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

Loading required package: stats4
Loading required package: tseries
Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Loading required package: TTR

Attaching package: 'TTR'

The following object is masked from 'package:gamlss.dist':

    DPO

Version 0.4-0 included new data defaults. See ?getSymbols.
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  iterations terminated because half-step sizes are very small
Warning in vglm.fitter(x = x, y = y, w = w, offset = offset, Xm2 = Xm2,  :
  some quantities such as z, residuals, SEs may be inaccurate due to convergence at a half-step

Error: processing vignette ‘tsglm.Rnw’ failed with diagnostics:
 chunk 42 (label = gcmr-package) 
Error in library("gcmr") : there is no package called 'gcmr'
Execution halted
Packages required but not available: ‘TSclust’ ‘longitudinalData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘forecast’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘tidyr’ ‘purrr’ ‘tibble’ ‘dplyr’ ‘tidyselect’

Packages suggested but not available for checking:
  ‘hts’ ‘nycflights13’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘MAPA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 26-38 (TSrepr_extentions.Rmd) 
Error: processing vignette ‘TSrepr_extentions.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘bfast’ ‘broom’ ‘ggplot2’

Packages suggested but not available for checking: ‘rgl’ ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotly’ ‘forecast’

Package suggested but not available for checking: ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘TSVC-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: TSVC
> ### Title: Tree-Structured Modelling of Varying Coefficients
> ### Aliases: TSVC print.TSVC
> 
> ### ** Examples
> 
> # Swiss Labour Market 
> library(AER)
Error in library(AER) : there is no package called ‘AER’
Execution halted
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  failed to tidy R code in chunk <fig1>
reason: Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 41-43 (example.Rmd) 
Error: processing vignette ‘example.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘mlrMBO’ ‘mlr’ ‘smoof’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘streamR’ ‘ggmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mapview’
Running examples in ‘uavRmp-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read_gpx
> ### Title: Read GPX file
> ### Aliases: read_gpx
> 
> ### ** Examples
> 
> ## for visualisation we are using mapview
> require(mapview)
Loading required package: mapview
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mapview’
> ## assign  GPX file
> gpxFN <- system.file("extdata", "flighttrack.gpx", package = "uavRmp")
> 
> ## read it
> gpx <- read_gpx(gpxFN, layers=c("tracks"))
> 
> ## plot it
> mapview::mapview(gpx)
Error in loadNamespace(name) : there is no package called ‘mapview’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘ggmap’ ‘dplyr’ ‘ggplot2’ ‘ggthemes’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘UBL-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImbC
> ### Title: Synthetic Imbalanced Data Set for a Multi-class Task
> ### Aliases: ImbC
> ### Keywords: datasets
> 
> ### ** Examples
> 
> require(ggplot2)
Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’
> data(ImbC)
> summary(ImbC)
       X1              X2         Class    
 Min.   :-13.5843   cat :300   normal:859  
 1st Qu.: -2.6930   dog :400   rare1 : 10  
 Median : -0.1592   fish:300   rare2 :131  
 Mean   : -0.1064                          
 3rd Qu.:  2.4633                          
 Max.   : 12.7836                          
> ggplot(data=ImbC, aes(x=X2, y=X1, color=Class))+geom_jitter()
Error in ggplot(data = ImbC, aes(x = X2, y = X1, color = Class)) : 
  could not find function "ggplot"
Execution halted
Packages required but not available: ‘ChemmineR’ ‘usethis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘readr’ ‘ggplot2’ ‘tibble’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘ukgasapi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dataItemExplorer
> ### Title: Data Item Explorer API
> ### Aliases: dataItemExplorer
> 
> ### ** Examples
> 
> # Specify the data item(s) to enquire from API
> dataitems <- c('Storage Injection, Actual',
+                'Storage Withdrawal, Actual')
> 
> # Initialise API (requires internet connection for this step)
> response <- dataItemExplorer(dataitems,
+                              fromdate = '2013-10-01',
+                              todate='2015-09-30')
*   Trying 40.127.139.252...
* TCP_NODELAY set
* Connected to marketinformation.natgrid.co.uk (40.127.139.252) port 80 (#0)
> POST /MIPIws-public/public/publicwebservice.asmx HTTP/1.1
Host: marketinformation.natgrid.co.uk
Accept: text/xml
Content-Type: application/soap+xml; charset=utf-8
Content-Length: 655

* upload completely sent off: 655 out of 655 bytes
< HTTP/1.1 200 OK
< Cache-Control: private, max-age=0
< Content-Length: 518779
< Content-Type: application/soap+xml; charset=utf-8
< Server: Microsoft-IIS/10.0
< X-AspNet-Version: 4.0.30319
< X-Powered-By: ASP.NET
< Set-Cookie: ARRAffinity=63b439f0293c59d3d2251ca7f54766e7c57d4a14f00f35ded75770f55ca5ec4d;Path=/;HttpOnly;Domain=marketinformation.natgrid.co.uk
< Date: Wed, 23 May 2018 05:02:11 GMT
< 
* Connection #0 to host marketinformation.natgrid.co.uk left intact
> 
> # Visualise the results on a chart
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘AdaptGauss’

Package suggested but not available for checking: ‘rgl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’ ‘DiagrammeR’

Package suggested but not available for checking: ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘UncertainInterval-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nlopt.ui.general
> ### Title: Function for the determination of the population thresholds an
> ###   inconclusive interval for bi-normal distributed test scores.
> ### Aliases: nlopt.ui.general
> 
> ### ** Examples
> 
> # A simple test model:
> nlopt.ui.general(Se = .55, Sp = .55,
+                  distribution = 'norm',
+                  parameters.d0 = c(mean = 0, sd = 1),
+                  parameters.d1 = c(mean = 1, sd = 1),
+                  overlap.interval=c(-2,3))
$status
[1] 4

$message
[1] "NLOPT_XTOL_REACHED: Optimization stopped because xtol_rel or xtol_abs (above) was reached."

$intersection
[1] 0.5

$results
exp.Sp.ui exp.Se.ui      mean        sd      mean        sd 
     0.55      0.55      0.00      1.00      1.00      1.00 

$solution
         L          U 
0.09307899 0.90692101 

> # Standard procedure when using a continous distribution:
> nlopt.ui.general(parameters.d0 = c(mean = 0, sd = 1),
+                  parameters.d1 = c(mean = 1.6, sd = 2))
Warning in nlopt.ui.general(parameters.d0 = c(mean = 0, sd = 1), parameters.d1 = c(mean = 1.6,  :
  More than one point of intersection. Point with highest density used.
$status
[1] 4

$message
[1] "NLOPT_XTOL_REACHED: Optimization stopped because xtol_rel or xtol_abs (above) was reached."

$intersection
[1] 1.194722

$results
exp.Sp.ui exp.Se.ui      mean        sd      mean        sd 
     0.55      0.55      0.00      1.00      1.60      2.00 

$solution
        L         U 
0.9107232 1.5315608 

> emp.AUC <- function(norm, abnorm) {
+   o = outer(abnorm, norm, "-")
+   mean((o > 0) + .5 * (o == 0))
+ }
> 
> library(MASS)
> library(car)
Error in library(car) : there is no package called ‘car’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 161-169 (UI-vignette.Rmd) 
Error: processing vignette ‘UI-vignette.Rmd’ failed with diagnostics:
there is no package called 'car'
Execution halted
Packages suggested but not available for checking: ‘tibble’ ‘ggforce’
Running ‘plot.R’ [0s/1s]
  Running ‘set_units.R’ [0s/1s]
  Running ‘testthat.R’ [1s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(units)
  
  Attaching package: 'units'
  
  The following object is masked from 'package:base':
  
      %*%
  
  > 
  > test_check("units")
  Error : cannot convert s into m
  ── 1. Error: type_sum is available for units objects (@test_misc.R#37)  ────────
  there is no package called 'tibble'
  1: library(tibble) at testthat/test_misc.R:37
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 274 SKIPPED: 3 FAILED: 1
  1. Error: type_sum is available for units objects (@test_misc.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error : cannot convert cm*km/h/s into cm/s
Quitting from lines 384-387 (measurement_units_in_R.Rmd) 
Error: processing vignette ‘measurement_units_in_R.Rmd’ failed with diagnostics:
there is no package called 'ggforce'
Execution halted
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking: ‘gapminder’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘dtplyr’ ‘purrr’ ‘tidyr’ ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘dplyr’ ‘readxl’ ‘tidyr’ ‘ggplot2’
Running examples in ‘unvotes-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: un_roll_calls
> ### Title: Data on each roll call of the United Nations General Assembly
> ### Aliases: un_roll_calls
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> library(dplyr)
Error in library(dplyr) : there is no package called ‘dplyr’
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 24-28 (unvotes.Rmd) 
Error: processing vignette ‘unvotes.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages suggested but not available for checking:
  ‘USAboundariesData’ ‘dplyr’ ‘leaflet’
Error in re-building vignettes:
  ...
Quitting from lines 23-30 (usaboundaries-sample-analysis.Rmd) 
Error: processing vignette ‘usaboundaries-sample-analysis.Rmd’ failed with diagnostics:
there is no package called 'dplyr'
Execution halted
Packages required but not available: ‘ggplot2’ ‘dplyr’ ‘purrr’

Package suggested but not available for checking: ‘tibble’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘car’ ‘data.tree’ ‘DiagrammeR’ ‘GGally’ ‘ggplot2’ ‘ggrepel’
  ‘ggridges’ ‘rio’ ‘viridis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘rematch2’ ‘styler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘usmap-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot_usmap
> ### Title: Conveniently plot basic US map
> ### Aliases: plot_usmap
> 
> ### ** Examples
> 
> plot_usmap()
Error in plot_usmap() : 
  Please install `ggplot2`. Use: install.packages("ggplot2")
Execution halted
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(usmap)
  > 
  > test_check("usmap")
  ── 1. Error: (unknown) (@test-plot.R#4)  ───────────────────────────────────────
  Please install `ggplot2`. Use: install.packages("ggplot2")
  1: plot_usmap() at testthat/test-plot.R:4
  2: stop("Please install `ggplot2`. Use: install.packages(\"ggplot2\")")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 52 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-plot.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 21-22 (introduction.Rmd) 
Error: processing vignette ‘introduction.Rmd’ failed with diagnostics:
Please install `ggplot2`. Use: install.packages("ggplot2")
Execution halted
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘dplyr’
Packages required but not available:
  ‘dplyr’ ‘readr’ ‘tibble’ ‘broom’ ‘ggplot2’

Packages suggested but not available for checking:
  ‘purrr’ ‘tidyr’ ‘DT’ ‘cowplot’ ‘dbplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘cowplot’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 80-92 (varrank.Rmd) 
Error: processing vignette ‘varrank.Rmd’ failed with diagnostics:
there is no package called 'caret'
Execution halted
Running examples in ‘VARSEDIG-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VARSEDIG
> ### Title: Variable selection to discriminate among taxonomic groups
> ### Aliases: VARSEDIG
> ### Keywords: VARSEDIG
> 
> ### ** Examples
> 
> 
> data(characiformes)
> 
> VARSEDIG(data = characiformes , variables = c("M2","M3","M4","M5","M6","M7","M8","M9","M10",
+ "M11","M12","M13","M14","M15","M16","M17","M18","M19","M20","M21","M22","M23",
+ "M24","M25","M26","M27","M28"), group="Species" , group1= "Moenkhausia oligolepis",
+ group2="Moenkhausia dichroura", LEGENDd=c("x='topright'", "legend = dati",
+ "col = COLORB", "lty=lty", "bty='n'", "cex=1.2", "text.font= 3"),
+ LEGENDs=c("x='topright'", "legend=unique(datosF[,'Group'])", "col = color1",
+ "pch = pcht", "bty='n'", "cex=1.2", "text.font=3"), LEGENDr=c("x='topright'",
+ "legend = dati", "col=col", "pch= c(16,16)", "bty='n'", "cex=1.2", "text.font=3"),
+ XLIMs=c(-1.2,1.2), YLIMs=c(-1.3,1.3), BIVTEST12=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), BIVTEST21=c("br=br", "cex=1.1",
+ "col=colbiv", "sub=sub", "Pcol=Pcol"), colbiv="blue")
dev.new(): using pdf(file="Rplots1.pdf")
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
Error in loadNamespace(name) : there is no package called ‘car’
Calls: VARSEDIG ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages suggested but not available for checking:
  ‘ggplot2’ ‘car’ ‘rgl’ ‘AER’
Error in re-building vignettes:
  ...
Loading required package: vcd
Loading required package: grid
Loading required package: gnm

Error: processing vignette ‘vcd-tutorial.Rnw’ failed with diagnostics:
 chunk 1 (label = preliminaries) 
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘dplyr’ ‘tibble’

Packages suggested but not available for checking:
  ‘adegenet’ ‘ggplot2’ ‘poppr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘purrr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘GGally’ ‘dplyr’ ‘broom’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘qgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘taxlist’ ‘plotKML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘lmerTest’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘VIM’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘ggbeeswarm’
Error in re-building vignettes:
  ...
Loading required package: sm
Package 'sm', version 2.2-5.5: type help(sm) for summary information

Error: processing vignette ‘methodComparison.Rnw’ failed with diagnostics:
 chunk 18 (label = showDiamond) 
Error in loadNamespace(name) : there is no package called ‘ggplot2’
Execution halted
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Packages required but not available: ‘ggplot2’ ‘tidyr’ ‘dplyr’ ‘purrr’

Packages suggested but not available for checking: ‘plotly’ ‘vdiffr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
          user system elapsed
ViSiElse 5.009  0.027   6.613
Packages suggested but not available for checking: ‘colourpicker’ ‘ggraph’
Packages required but not available: ‘ggplot2’ ‘readxl’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘vlad-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: calceo
> ### Title: Compute Expected minus Observed value
> ### Aliases: calceo
> ### Keywords: keyword1 keyword2
> 
> ### ** Examples
> 
> library("vlad")
> # see Steiner (2014) p. 234
> coeff <- c("(Intercept)"=-3.68, "Parsonnet"=0.077)
> # penalty reward for death (E-O scores multiplied with -1 to get O-E scores)
> calceo(df=data.frame(as.integer(0), 1), coeff=coeff)*-1
[1] 0.9753976
> calceo(df=data.frame(as.integer(50), 1), coeff=coeff)*-1
[1] 0.4576021
> # penalty reward for survival
> calceo(df=data.frame(as.integer(0), 0), coeff=coeff)*-1
[1] -0.02460243
> calceo(df=data.frame(as.integer(50), 0), coeff=coeff)*-1
[1] -0.5423979
> 
> # Plot a VLAD/CRAM chart
> library("spcadjust")
> data("cardiacsurgery")
> cardiacsurgery <- dplyr::mutate(cardiacsurgery, phase=factor(ifelse(date < 2*365, "I", "II")))
Error in loadNamespace(name) : there is no package called ‘dplyr’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Packages required but not available: ‘ggmap’ ‘marmap’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘lmerTest’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘VoxR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: VoxR-package
> ### Title: Metrics extraction of trees from T-LiDAR data
> ### Aliases: VoxR-package VoxR
> ### Keywords: package 3d point cloud LiDAR
> 
> ### ** Examples
> 
> data(treecloud)
> 
> #-voxelisation using the vox function
> 
> treecloud_vox <- vox(treecloud,res=0.02)
> 
> #-visualisation
> 
> require(rgl)
Loading required package: rgl
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘rgl’
> library(rgl)
Error in library(rgl) : there is no package called ‘rgl’
Execution halted
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘viridis’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘car’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘plotKML’ ‘Hmisc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Quitting from lines 35-60 (vtreatRareLevels.Rmd) 
Error: processing vignette ‘vtreatRareLevels.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘tibble’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘bayesplot’ ‘rstan’ ‘dplyr’ ‘ggplot2’

Package suggested but not available for checking: ‘diagis’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘ggplot2’ ‘shinystan’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘leaflet’ ‘DT’ ‘spocc’ ‘dplyr’ ‘leaflet.extras’

Package suggested but not available for checking: ‘RSelenium’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘riskRegression’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Sim.DiffProc’

Packages suggested but not available for checking: ‘ggplot2’ ‘Rraven’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tiger’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘geojsonio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘purrr’ ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘cobalt’

Package suggested but not available for checking: ‘jtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘wellknown-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: multilinestring
> ### Title: Make WKT multilinestring objects
> ### Aliases: multilinestring
> 
> ### ** Examples
> 
> ## empty multilinestring
> multilinestring("empty")
[1] "MULTILINESTRING EMPTY"
> # multilinestring("stuff")
> 
> # character string
> x <- "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> multilinestring(x)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> 
> # data.frame
> df <- data.frame(long = c(30, 45, 10), lat = c(20, 40, 40))
> df2 <- data.frame(long = c(15, 40, 10), lat = c(5, 10, 20))
> multilinestring(df, df2, fmt=0)
[1] "MULTILINESTRING ((30 20, 45 40, 10 40), (15 5, 40 10, 10 20))"
> lint(multilinestring(df, df2, fmt=0))
[1] TRUE
> wktview(multilinestring(df, df2), zoom=3)
Error: Please install leaflet
Execution halted
Package required but not available: ‘NPflow’

Package suggested but not available for checking: ‘EdSurvey’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘CRTgeeDR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘tidyr’ ‘tidytext’ ‘purrr’ ‘broom’

Packages suggested but not available for checking:
  ‘ggraph’ ‘gapminder’ ‘fuzzyjoin’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘drc’ ‘imputeTestbench’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘ggplot2’ ‘rgl’ ‘leaflet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dbplyr’ ‘dplyr’ ‘purrr’ ‘tidyr’

Package suggested but not available for checking: ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘openair’ ‘dplyr’ ‘leaflet’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘ggplot2’ ‘DT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘readxl’ ‘nycflights13’
Running examples in ‘writexl-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: write_xlsx
> ### Title: Export to xlsx
> ### Aliases: write_xlsx writexl
> 
> ### ** Examples
> 
> # Roundtrip example
> tmp <- write_xlsx(iris)
> readxl::read_xlsx(tmp)
Error in loadNamespace(name) : there is no package called ‘readxl’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running ‘spelling.R’ [0s/1s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(writexl)
  > 
  > test_check("writexl")
  ── 1. Error: Performance is OK (@test-performance.R#4)  ────────────────────────
  there is no package called 'nycflights13'
  1: writexl::write_xlsx(nycflights13::flights) at testthat/test-performance.R:4
  2: is.data.frame(x)
  3: nycflights13::flights
  4: getExportedValue(pkg, name)
  5: asNamespace(ns)
  6: getNamespace(ns)
  7: tryCatch(loadNamespace(name), error = function(e) stop(e))
  8: tryCatchList(expr, classes, parentenv, handlers)
  9: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  10: value[[3L]](cond)
  
  ── 2. Error: Types roundtrip properly (@test-types.R#14)  ──────────────────────
  there is no package called 'readxl'
  1: expect_equal(df, as.data.frame(roundtrip(df))) at testthat/test-types.R:14
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: as.data.frame(roundtrip(df))
  5: roundtrip(df)
  6: readxl::read_xlsx at testthat/test-types.R:4
  7: getExportedValue(pkg, name)
  8: asNamespace(ns)
  9: getNamespace(ns)
  10: tryCatch(loadNamespace(name), error = function(e) stop(e))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Error: Performance is OK (@test-performance.R#4) 
  2. Error: Types roundtrip properly (@test-types.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘car’ ‘ez’
Error in re-building vignettes:
  ...
Loading required package: WRS2
Loading required package: beanplot
Loading required package: car
Loading required package: MASS
Loading required package: colorspace
Loading required package: reshape
Loading required package: ez
Loading required package: MBESS
Quitting from lines 390-393 (WRS2.Rnw) 
Error: processing vignette ‘WRS2.Rnw’ failed with diagnostics:
could not find function "Anova"
Execution halted
Packages required but not available:
  ‘ggplot2’ ‘caret’ ‘dplyr’ ‘EnvStats’ ‘forecast’ ‘purrr’ ‘tidyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘tigris’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘btergm’ ‘GERGM’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘bupaR’ ‘dplyr’ ‘tidyr’ ‘purrr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘ggplot2’ ‘DiagrammeR’
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘tidyr’ ‘ggrepel’ ‘ggnetwork’

Packages suggested but not available for checking:
  ‘treemapify’ ‘ggraph’ ‘ggbio’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: XLConnect
Loading required package: XLConnectJars
XLConnect 0.2-15 by Mirai Solutions GmbH [aut],
  Martin Studer [cre],
  The Apache Software Foundation [ctb, cph] (Apache POI),
  Graph Builder [ctb, cph] (Curvesapi Java library)
http://www.mirai-solutions.com
https://github.com/miraisolutions/xlconnect
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by org.apache.poi.util.DocumentHelper (file:/home/hornik/tmp/R.check/r-devel-gcc/Work/build/Packages/XLConnect/java/poi-ooxml-3.17.jar) to method com.sun.org.apache.xerces.internal.util.SecurityManager.setEntityExpansionLimit(int)
WARNING: Please consider reporting this to the maintainers of org.apache.poi.util.DocumentHelper
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: ggplot2
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘ggplot2’

Error: processing vignette ‘XLConnect.Rnw’ failed with diagnostics:
 chunk 20 (label = AdvancedExampleP5) 
Error in ggplot(gcurr, aes(Date, Value, colour = Currency)) : 
  could not find function "ggplot"
Execution halted
Package required but not available: ‘readr’

Package suggested but not available for checking: ‘car’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘Hmisc’ ‘dplyr’ ‘readr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘ggplot2’ ‘dplyr’ ‘ggforce’ ‘purrr’ ‘readr’ ‘tibble’ ‘tidyr’ ‘vpc’

Package suggested but not available for checking: ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘colourpicker’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘readr’

Packages suggested but not available for checking: ‘DT’ ‘ggplot2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘SACCR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘broom’ ‘dplyr’ ‘tibble’ ‘tidyr’ ‘pROC’ ‘tidyselect’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘DT’ ‘ggplot2’ ‘plotly’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘ggetho’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘Zelig’

Package suggested but not available for checking: ‘zeligverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘dplyr’ ‘Zelig’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘AER’ ‘dplyr’

Packages suggested but not available for checking:
  ‘tidyverse’ ‘ZeligChoice’ ‘ZeligEI’ ‘zeligverse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available:
  ‘dplyr’ ‘purrr’ ‘tibble’ ‘WhatIf’ ‘Zelig’ ‘ZeligChoice’ ‘ZeligEI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: TSP
Loading required package: gtools
Loading required package: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Loading required package: grid
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 160-190 (selected_features.Rmd) 
Error: processing vignette ‘selected_features.Rmd’ failed with diagnostics:
there is no package called 'ggplot2'
Execution halted
Packages required but not available: ‘tidyr’ ‘ggplot2’ ‘tibble’ ‘dplyr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘ggplot2’

Package suggested but not available for checking: ‘zdat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘car’ ‘geomorph’ ‘ggplot2’ ‘readxl’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running examples in ‘zoocat-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gmon_trans
> ### Title: Tools for plottin 'zoocat' objects with ggplot2
> ### Aliases: gmon_trans scale_x_gmon scale_y_gmon
> 
> ### ** Examples
> 
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
Execution halted
Package required but not available: ‘rfigshare’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘rARPACK’ ‘sparseLDA’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘AdaptFit/R/aspm.R’:
  assign("group.vec.Handan", group.vec, pos = 1)
  assign("X.Declan", X, pos = 1)
  assign("Z.Jaida", Z, pos = 1)
Namespace in Imports field not imported from: ‘Benchmarking’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Namespace in Imports field not imported from: ‘filehash’
  All declared Imports should be used.
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ADM3.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘fields’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘assertthat’ ‘tibble’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error: processing vignette 'AccumulatedLocalEffectPlot.ltx' failed with diagnostics:
Running 'texi2dvi' on 'AccumulatedLocalEffectPlot.ltx' failed.
LaTeX errors:
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package inputenc Error: Unicode character ̂ (U+302)
(inputenc)                not set up for use with LaTeX.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
! Package
Execution halted
Namespaces in Imports field not imported from:
  ‘rjson’ ‘xml2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘devtools’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data  15.6Mb
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/amei.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘unmarked’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘magrittr’
  All declared Imports should be used.
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rgdal’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   4.7Mb
Namespace in Imports field not imported from: ‘caret’
  All declared Imports should be used.
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
Found the following significant warnings:
  Warning: namespace ‘RPostgreSQL’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-clang/antaresViz.Rcheck/00install.out’ for details.
Running examples in ‘aop-Ex.R’ failed
The error most likely occurred in:

> ### Name: aop_backdoor
> ### Title: Backdoor Causal Network Analysis for AOPs
> ### Aliases: aop_backdoor
> 
> ### ** Examples
> 
> steatosis_json_file <- system.file("extdata", "steatosis_aop_json.cyjs",
+ package = "aop")
> steatosis_aop <- convert_cytoscape_to_aop(steatosis_json_file)
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
unsupported SEXPTYPE: 19
> steatosis_aop_graph <- convert_aop_to_graph(steatosis_aop)
Error in (function (cl, name, valueClass)  : 
  assignment of an object of class “NULL” is not valid for @‘nodes’ in an object of class “graphNEL”; is(value, "vector") is not TRUE
Calls: convert_aop_to_graph ... new -> initialize -> initialize -> .local -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-50 (aop.Rmd) 
Error: processing vignette 'aop.Rmd' failed with diagnostics:
assignment of an object of class "NULL" is not valid for @'nodes' in an object of class "graphNEL"; is(value, "vector") is not TRUE
Execution halted
Namespace in Imports field not imported from: ‘pls’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Namespace in Imports field not imported from: ‘testthat’
  All declared Imports should be used.
runAPSIM: warning in scan(reports_file[i], "", sep = "", skip =
  length(temp), nline = 1): partial argument match of 'nline' to
  'nlines'
runAPSIM: no visible global function definition for ‘write.table’
runAPSIM: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table write.table
Consider adding
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/aqr.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘DT’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.1Mb
    testScripts   1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Namespace in Imports field not imported from: ‘stringi’
  All declared Imports should be used.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.6Mb
Namespace in Imports field not imported from: ‘tidyr’
  All declared Imports should be used.
File ‘audio/libs/audio.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘abind’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespace in Imports field not imported from: ‘purrr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
installed size is 67.2Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/BAMBI.Rcheck/00install.out’ for details.
installed size is 103.4Mb
  sub-directories of 1Mb or more:
    libs  102.6Mb
Namespace in Imports field not imported from: ‘stringr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.8Mb
Namespace in Imports field not imported from: ‘dplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘MatrixModels’
  All declared Imports should be used.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  16.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 58.0Mb
  sub-directories of 1Mb or more:
    libs  57.2Mb
Namespace in Imports field not imported from: ‘inline’
  All declared Imports should be used.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  24.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    ex-data   4.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 92.2Mb
  sub-directories of 1Mb or more:
    libs  92.1Mb
Namespaces in Imports field not imported from:
  ‘ggfortify’ ‘ggplot2’ ‘matrixStats’ ‘reshape2’ ‘scales’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘ggplot2’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘readxl’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 98.2Mb
  sub-directories of 1Mb or more:
    libs  96.8Mb
Namespace in Imports field not imported from: ‘rstantools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘chron’ ‘colorspace’ ‘gtable’ ‘htmltools’ ‘htmlwidgets’
  ‘httpuv’ ‘magrittr’ ‘munsell’ ‘plyr’ ‘scales’ ‘stringi’ ‘xtable’
  ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crochet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
Error in re-building vignettes:
  ...
Loading required package: leaps
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SimExperimentBICq.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 150.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 144.8Mb
  sub-directories of 1Mb or more:
    include  144.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.0Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/bigrquery.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘lattice’ ‘zoo’
  All declared Imports should be used.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.1Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   8.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Namespace in Imports field not imported from: ‘tibble’
  All declared Imports should be used.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespace in Imports field not imported from: ‘utils’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Running examples in ‘bit-Ex.R’ failed
The error most likely occurred in:

> ### Name: regtest.bit
> ### Title: Regressiontests for bit
> ### Aliases: regtest.bit
> ### Keywords: classes logic
> 
> ### ** Examples
> 
>   if (regtest.bit()){
+     message("regtest.bit is OK")
+   }else{
+     message("regtest.bit failed")
+   }

 *** caught segfault ***
address 0x13010f7c, cause 'memory not mapped'

Traceback:
 1: `[.bit`(b, i)
 2: b[i]
 3: unattr(b[i])
 4: regtest.bit()
An irrecoverable exception occurred. R is aborting now ...
Package suggested but not available for checking: ‘RQuantLib’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘purrr’ ‘rlang’ ‘tibble’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RGtk2’ ‘cairoDevice’ ‘ergm’ ‘foreign’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘haven’ ‘plot3D’ ‘plot3Drgl’ ‘rgl’ ‘sna’ ‘statnet.common’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
installed size is 43.7Mb
  sub-directories of 1Mb or more:
    libs  42.6Mb
Package suggested but not available for checking: ‘PopGenome’
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Namespace in Imports field not imported from: ‘descriptr’
  All declared Imports should be used.
Running examples in ‘blsAPI-Ex.R’ failed
The error most likely occurred in:

> ### Name: blsQCEW
> ### Title: Request QCEW Data from the U.S. Bureau Of Labor Statistics Open
> ###   Data Access
> ### Aliases: blsQCEW
> ### Keywords: bls economics
> 
> ### ** Examples
> 
> ## These examples are taken from the sample code examples found at: 
> ## <https://www.bls.gov/cew/doc/access/data_access_examples.htm>
> 
> ## Area Data Request
> 
> ## Required parameters are:
> ##  * year
> ##  * quarter
> ##  * area
> 
> ## Example: Request the first quarter of 2013 for the state of Michigan
> MichiganData <- blsQCEW('Area', year='2013', quarter='1', area='26000')
Warning in file(file, "rt") :
  cannot open URL 'https://data.bls.gov/cew/data/api/2013/1/area/26000.csv': HTTP status was '403 Forbidden'
Error in file(file, "rt") : 
  cannot open the connection to 'https://www.bls.gov/cew/data/api/2013/1/area/26000.csv'
Calls: blsQCEW -> read.csv -> read.table -> file
Execution halted
Running examples in ‘blscrapeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: qcew_api
> ### Title: Request data from the Quarterly Census of Employment and Wages.
> ### Aliases: qcew_api
> ### Keywords: api bls cpi economics inflation unemployment
> 
> ### ** Examples
> 
> 
> # A request for the employment levels and wages for NIACS 5112: Software Publishers.
> dat <- qcew_api(year=2015, qtr="A", slice="area", sliceCode="US000")
Please set a numeric year.
Trying BLS servers...
URL caused a warning. Please check your parameters and try again: https://data.bls.gov/cew/data/api/2015/A/area/US000.csv
Error in qcew_api(year = 2015, qtr = "A", slice = "area", sliceCode = "US000") : 
  object 'qcewDat' not found
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blscrapeR)
  > 
  > test_check("blscrapeR")
  ── 1. Error: (unknown) (@test_qcew_api.R#8)  ───────────────────────────────────
  cannot open URL 'https://data.bls.gov/cew/data/api/2013/1/industry/5112.csv'
  1: download.file(url, temp, quiet = TRUE) at testthat/test_qcew_api.R:8
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_qcew_api.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘plm’
  All declared Imports should be used.
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/bnlearn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./sampling.h:84:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BNSP.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
Namespace in Imports field not imported from: ‘rappdirs’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘yaml’
  All declared Imports should be used.
installed size is 376.8Mb
  sub-directories of 1Mb or more:
    include    3.2Mb
    lib      373.3Mb
installed size is 84.6Mb
  sub-directories of 1Mb or more:
    libs  84.1Mb
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Namespaces in Imports field not imported from:
  ‘CCA’ ‘brainR’ ‘elasticnet’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sp’
  All declared Imports should be used.
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  29.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘profileModel’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R     3.5Mb
    doc   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    bin    2.3Mb
    doc    1.1Mb
    libs   2.3Mb
Namespaces in Imports field not imported from:
  ‘rworldxtra’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/BSquare.Rcheck/00install.out’ for details.
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  31.2Mb
installed size is 98.7Mb
  sub-directories of 1Mb or more:
    libs  98.1Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Namespace in Imports field not imported from: ‘markdown’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Matrix’
  All declared Imports should be used.
Found the following significant warnings:
  slpcovis.cpp:381:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/catlearn.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
ConstructModel: warning in AddDynamicRegression(ss, formula, data =
  data, sigma.mean.prior = sigma.mean.prior): partial argument match of
  'sigma.mean.prior' to 'sigma.mean.prior.DEPRECATED'
Namespace in Imports field not imported from: ‘prettydoc’
  All declared Imports should be used.
estim.regul: warning in matrix(res, nc = length(grid2)): partial
  argument match of 'nc' to 'ncol'
comput: no visible global function definition for ‘cor’
img.estim.regul: no visible global function definition for ‘par’
img.estim.regul: no visible global function definition for ‘image’
img.estim.regul: no visible global function definition for
  ‘heat.colors’
img.estim.regul: no visible global function definition for ‘axis’
img.estim.regul: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘par’
img.matcor: no visible global function definition for ‘image’
img.matcor: no visible global function definition for ‘box’
img.matcor: no visible global function definition for ‘abline’
img.matcor: no visible global function definition for ‘layout’
loo: no visible global function definition for ‘cor’
matcor: no visible global function definition for ‘cor’
plt.cc: no visible global function definition for ‘par’
plt.cc: no visible global function definition for ‘layout’
plt.indiv: no visible global function definition for ‘plot’
plt.indiv: no visible global function definition for ‘text’
plt.indiv: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘plot’
plt.var: no visible global function definition for ‘points’
plt.var: no visible global function definition for ‘text’
plt.var: no visible global function definition for ‘abline’
plt.var: no visible global function definition for ‘lines’
rcc: no visible global function definition for ‘var’
rcc: no visible global function definition for ‘cov’
Undefined global functions or variables:
  abline axis box cor cov heat.colors image layout lines par plot
  points text var
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "layout",
             "lines", "par", "plot", "points", "text")
  importFrom("stats", "cor", "cov", "var")
to your NAMESPACE file.
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/CCMnet.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘units’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lazyeval’ ‘purrr’ ‘roxygen2’
  All declared Imports should be used.
Running examples in ‘CDECRetrieve-Ex.R’ failed
The error most likely occurred in:

> ### Name: cdec_rt
> ### Title: Get a rating table
> ### Aliases: cdec_rt
> 
> ### ** Examples
> 
> cdec_rt("abj") # get the stage to rating curve for ABJ
Error in open.connection(x, "rb") : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: cdec_rt ... %in% -> cdec_rt_list -> <Anonymous> -> read_html.default
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 55-69 (CDECRetrieve.Rmd) 
Error: processing vignette 'CDECRetrieve.Rmd' failed with diagnostics:
Timeout was reached: Connection timed out after 10000 milliseconds
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.1Mb
Namespace in Imports field not imported from: ‘data.table’
  All declared Imports should be used.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
Namespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/changepoint.np.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘datasets’ ‘foreach’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘dbplyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gamlss.dist’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘knitr’ ‘tools’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.7Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘httr’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘stringr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘circlize’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/cld_3/protos/feature_extractor.pb.h’
  ‘src/cld_3/protos/sentence.pb.h’ ‘src/cld_3/protos/task_spec.pb.h’
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Namespaces in Imports field not imported from:
  ‘scales’ ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  ./networkCliqueMSR.h:4:9: warning: 'NETWORKClIQUEMSR_H' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/data/gannet/ripley/R/packages/tests-clang/cliqueMS.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘infuser’ ‘purrr’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data     3.5Mb
    exdata   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
Quitting from lines 30-36 (coala-data-import.Rmd) 
Error: processing vignette 'coala-data-import.Rmd' failed with diagnostics:
there is no package called 'PopGenome'
Execution halted
Namespaces in Imports field not imported from:
  ‘graphics’ ‘htmltools’ ‘pander’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘memoise’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘geometry’ ‘parallel’ ‘plot3D’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘flashClust’ ‘speedglm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘crayon’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rscala’
Namespaces in Imports field not imported from:
  ‘PearsonDS’ ‘VGAM’ ‘actuar’ ‘fExtremes’ ‘rmutil’
  All declared Imports should be used.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/CompRandFld.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
Namespace in Imports field not imported from: ‘graphics’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘MASS’ ‘geepack’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘knitr’
  All declared Imports should be used.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Namespaces in Imports field not imported from:
  ‘Rtsne’ ‘scatterplot3d’
  All declared Imports should be used.
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Namespace in Imports field not imported from: ‘xtable’
  All declared Imports should be used.
Package in Depends field not imported from: ‘calibrate’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   5.2Mb
Namespace in Imports field not imported from: ‘maps’
  All declared Imports should be used.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Namespace in Imports field not imported from: ‘gstat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘misc3d’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    libs  38.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
QR.cd: no visible global function definition for ‘quantile’
QR.lasso.cd: no visible global function definition for ‘quantile’
cqr.cd: no visible global function definition for ‘quantile’
cqr.lasso.cd: no visible global function definition for ‘quantile’
cqr.lasso.mm: no visible global function definition for ‘quantile’
cqr.mm: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  quantile
Consider adding
  importFrom("stats", "quantile")
to your NAMESPACE file.
File ‘cqrReg/libs/cqrReg.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 69-75 (dependence_trees.Rmd) 
Error: processing vignette 'dependence_trees.Rmd' failed with diagnostics:
'x' must be atomic
Execution halted
Note: found 11 marked Latin-1 strings
  Note: found 57 marked UTF-8 strings
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘AnnotationDbi’ ‘clusterProfiler’ ‘org.Hs.eg.db’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘r6extended’
  All declared Imports should be used.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
Namespace in Imports field not imported from: ‘httpcode’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘qte’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    shp   7.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data  10.9Mb
Note: found 59670 marked Latin-1 strings
  Note: found 16 marked UTF-8 strings
Found the following significant warnings:
  ./ctl.h:38:23: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  ./ctl.h:36:25: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/ctl.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘tea’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    extdata  31.9Mb
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘stats’ ‘utils’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   5.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Namespace in Imports field not imported from: ‘titanic’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DBI’ ‘Demerelate’ ‘misc3d’ ‘plotly’ ‘quadprog’ ‘rgl’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘curl’
  All declared Imports should be used.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    java  15.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
.onLoad : <anonymous>: no visible global function definition for
  ‘read.table’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbConnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbListTables’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbExistsTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbReadTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbWriteTable’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbDisconnect’
.onLoad : <anonymous>: no visible global function definition for
  ‘dbRemoveTable’
Undefined global functions or variables:
  dbConnect dbDisconnect dbExistsTable dbListTables dbReadTable
  dbRemoveTable dbWriteTable read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 61.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  59.3Mb
Namespace in Imports field not imported from: ‘RCurl’
  All declared Imports should be used.
browse: no visible global function definition for ‘slot’
browse: no visible global function definition for ‘page’
default.options: no visible binding for global variable ‘object.size’
heat.view: no visible global function definition for ‘head’
heat.view: no visible global function definition for ‘tail’
whos: no visible global function definition for ‘slotNames’
whos : <anonymous> : <anonymous>: no visible global function definition
  for ‘slot’
Undefined global functions or variables:
  head object.size page slot slotNames tail
Consider adding
  importFrom("methods", "slot", "slotNames")
  importFrom("utils", "head", "object.size", "page", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.1Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘gridExtra’ ‘latticeExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘CDM’
  All declared Imports should be used.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Namespace in Imports field not imported from: ‘oz’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.8Mb
'library' or 'require' call to ‘UScensus2010’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Namespace in Imports field not imported from: ‘UScensus2010’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘JavaGD’ ‘OpenStreetMap’ ‘maptools’ ‘rgdal’ ‘scales’ ‘sp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Bootstrapping.CI: no visible global function definition for ‘quantile’
D.Jost: no visible global function definition for ‘read.table’
D.Jost: no visible global function definition for ‘write.table’
Dv.locis.corrected.calc: no visible global function definition for
  ‘p.adjust’
Gst.Nei: no visible global function definition for ‘read.table’
Gst.Nei: no visible global function definition for ‘write.table’
H.out: no visible global function definition for ‘write.table’
Hardy.calc: no visible global function definition for ‘chisq.test’
critical.ci.values: no visible global function definition for
  ‘quantile’
inputformat: no visible global function definition for ‘read.table’
inputformat: no visible global function definition for ‘write.table’
over.all.pops: no visible global function definition for ‘write.table’
p.value.correcture: no visible global function definition for
  ‘p.adjust’
pair.pops: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  chisq.test p.adjust quantile read.table write.table
Consider adding
  importFrom("stats", "chisq.test", "p.adjust", "quantile")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘mvtnorm’
  All declared Imports should be used.
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DEploid.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.6Mb
Packages suggested but not available for checking: ‘gurobi’ ‘Rcplex’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  17.4Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Namespace in Imports field not imported from: ‘mgcv’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc   9.3Mb
Namespace in Imports field not imported from: ‘gplots’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    include  16.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.8Mb
Namespace in Imports field not imported from: ‘randomForest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘GOstats’ ‘caTools’ ‘fdrtool’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   5.8Mb
Namespaces in Imports field not imported from:
  ‘tidyr’ ‘tidyverse’
  All declared Imports should be used.
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’ ‘tidyverse’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.5Mb
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/DPWeibull.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘readr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shapefiles’
  All declared Imports should be used.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.1Mb
Namespace in Imports field not imported from: ‘xml2’
  All declared Imports should be used.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  16.9Mb
Namespaces in Imports field not imported from:
  ‘maptools’ ‘tools’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘Rdpack’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘reshape2’ ‘scales’ ‘xtable’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘base64enc’ ‘knitr’ ‘markdown’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    hac    4.0Mb
Namespace in Imports field not imported from: ‘pander’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dae’ ‘dplyr’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    1.2Mb
installed size is 53.9Mb
  sub-directories of 1Mb or more:
    libs  53.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data  11.5Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    xsd   5.4Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.3Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.5Mb
Note: found 23639 marked Latin-1 strings
Namespaces in Imports field not imported from:
  ‘BiocParallel’ ‘broom’ ‘reshape2’ ‘rmarkdown’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  input2.c:767:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/epanet2toolkit.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘ROCR’ ‘c060’ ‘methods’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘colorspace’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘llogistic’ ‘logitnorm’
  All declared Imports should be used.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
Namespace in Imports field not imported from: ‘signal’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘searcher’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘modelr’
  All declared Imports should be used.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘msm’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘EnvStats’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
Namespaces in Imports field not imported from:
  ‘curl’ ‘openxlsx’ ‘stringr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘CodeDepends’ ‘DT’ ‘PKI’ ‘shinycssloaders’ ‘tictoc’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘polynom’
  All declared Imports should be used.
print.cdf : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.cdf: warning in get("x", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.cdf: warning in get("y", env = environment(x)): partial argument
  match of 'env' to 'envir'
print.ogive : numform: warning in formatC(x, dig = digits): partial
  argument match of 'dig' to 'digits'
print.ogive: warning in get("x", env = environment(x)): partial
  argument match of 'env' to 'envir'
print.ogive: warning in get("y", env = environment(x)): partial
  argument match of 'env' to 'envir'
quantile.expert: warning in formatC(paste(100 * probs, "%", sep = ""),
  format = "fg", wid = 1, digits = dig): partial argument match of
  'wid' to 'width'
MS: no visible global function definition for ‘tail’
Undefined global functions or variables:
  tail
Consider adding
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘gtools’
  All declared Imports should be used.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespace in Imports field not imported from: ‘refund’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forcats’ ‘formula.tools’
  All declared Imports should be used.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.1Mb
Namespace in Imports field not imported from: ‘rgdal’
  All declared Imports should be used.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-clang/FastRWeb.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘whisker’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
installed size is 53.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  50.6Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   7.1Mb
Namespaces in Imports field not imported from:
  ‘cellranger’ ‘knitr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘httr’
  All declared Imports should be used.
Found the following significant warnings:
  ff.cpp:256:16: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ff.cpp:256:54: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/ff.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespace in Imports field not imported from: ‘desc’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘XML’ ‘gglasso’ ‘methods’
  All declared Imports should be used.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R   6.4Mb
Namespace in Imports field not imported from: ‘survival’
  All declared Imports should be used.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    fonts   6.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    fonts   6.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespaces in Imports field not imported from:
  ‘base’ ‘pbapply’ ‘stringr’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Running examples in ‘FREddyPro-Ex.R’ failed
The error most likely occurred in:

> ### Name: buildTimestamp
> ### Title: Build a timestamp
> ### Aliases: buildTimestamp
> 
> ### ** Examples
> 
> ## Load the data
> data(fluxes)
> 
> ## Clean fluxes
> fluxes=cleanFluxes(fluxes,sdCor=TRUE,sdTimes=3,timesList=3,distCor=TRUE,
+                    thresholdList=list(H=c(-100,1000),LE=c(-100,1000)))	
> 
> ## Remove some line as an example
> fluxes=fluxes[-c(832,833,834,835,840,953),]
> 
> ## Create timestamp from date and time
> fluxes=createTimestamp(fluxes)
> 
> ## Now fill the gap timestmaps with NA's
> fluxes=fillTimestamp(fluxes,flux=TRUE)
[1] Discontinuity in 3 instances
[1] 2014-06-14 03:30:00 UTC 2014-06-14 06:00:00 UTC 2014-06-16 14:30:00 UTC
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: fillTimestamp ... shift_time -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
Found the following significant warnings:
  psplines.c:975:16: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  psplines.c:1087:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/freeknotsplines.Rcheck/00install.out’ for details.
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.7Mb
Package suggested but not available for checking: ‘dggrids’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
Namespaces in Imports field not imported from:
  ‘R.utils’ ‘grDevices’ ‘graphics’ ‘matrixStats’ ‘stats’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 : *Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
4 : *Loading required namespace: funHDDC
 *Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
 * *Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!
Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!
 *

Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
fuzzyBHexact: warning in round(pvals, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = dp): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(p.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.minus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(a.plus, d = 4): partial argument match
  of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.minus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(new.p.plus, d = 4): partial argument
  match of 'd' to 'digits'
fuzzyBHexact: warning in round(pvals, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(pprev, d = 4): partial argument match of
  'd' to 'digits'
fuzzyBHexact: warning in round(tau, d = 4): partial argument match of
  'd' to 'digits'
probRejTies: no visible binding for global variable ‘nn’
Undefined global functions or variables:
  nn
Namespace in Imports field not imported from: ‘scales’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘maptools’ ‘rgeos’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘gamlss’
  All declared Imports should be used.
finterp.data.frame: no visible global function definition for
  ‘as.formula’
finterp.data.frame: no visible global function definition for ‘terms’
finterp.data.frame: no visible global function definition for
  ‘model.matrix’
finterp.data.frame: no visible global function definition for
  ‘model.frame’
finterp.default: no visible global function definition for ‘terms’
finterp.default: no visible global function definition for
  ‘model.matrix’
finterp.default: no visible global function definition for
  ‘model.frame’
gamlss.nl: no visible global function definition for ‘nlm’
nl: no visible global function definition for ‘is’
nlgamlss: no visible global function definition for ‘NO’
nlgamlss: no visible global function definition for ‘as.gamlss.family’
nlgamlss: no visible global function definition for ‘nlm’
nlgamlss: no visible global function definition for ‘cov2cor’
summary.nlgamlss: no visible global function definition for ‘coef’
summary.nlgamlss: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  NO as.formula as.gamlss.family coef cov2cor is model.frame
  model.matrix nlm pnorm terms
Consider adding
  importFrom("methods", "is")
  importFrom("stats", "as.formula", "coef", "cov2cor", "model.frame",
             "model.matrix", "nlm", "pnorm", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   8.6Mb
installed size is 63.1Mb
  sub-directories of 1Mb or more:
    libs  62.7Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     73.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘roxygen2’ ‘testthat’ ‘utils’ ‘withr’
  All declared Imports should be used.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  16.3Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/gdmp.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘NMF’ ‘RColorBrewer’ ‘VennDiagram’ ‘clValid’ ‘data.table’ ‘grid’
  ‘gtools’ ‘pca3d’ ‘rmarkdown’ ‘scales’ ‘shinydashboard’ ‘shinyjs’
  ‘statmod’ ‘stringr’
  All declared Imports should be used.
Running examples in ‘genderBR-Ex.R’ failed
The error most likely occurred in:

> ### Name: map_gender
> ### Title: Map the use of Brazilian first names by gender and by state
> ### Aliases: map_gender
> 
> ### ** Examples
> 
> # Map the use of the name 'Joao' for
> # males in Brazil by state
> map_gender('Joao', gender = 'm')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10000 milliseconds
Calls: map_gender ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.1Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   3.7Mb
installed size is 26.1Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         3.5Mb
    extdata   1.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.8Mb
Namespace in Imports field not imported from: ‘velociraptr’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘utils’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘shinydashboard’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotly’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggforce’ ‘plyr’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Namespaces in Imports field not imported from:
  ‘GGEBiplotGUI’ ‘gge’ ‘utils’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plyr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘grid’ ‘rstan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘lazyeval’ ‘readr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridGraphics’ ‘rvcheck’ ‘scales’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 101-103 (ggimage.Rmd) 
Error: processing vignette 'ggimage.Rmd' failed with diagnostics:
Failed to download https://raw.githubusercontent.com/ionic-team/ionicons/master/png/512/pie-graph.png (HTTP 404)
Execution halted
Namespaces in Imports field not imported from:
  ‘XML’ ‘mapproj’ ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘NHANES’ ‘gridExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gcookbook’ ‘ggthemes’ ‘moonBook’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘grid’ ‘gridExtra’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘Hmisc’ ‘colourpicker’ ‘dplyr’ ‘ggrepel’ ‘grDevices’ ‘gridExtra’
  ‘lazyeval’ ‘markdown’ ‘plotly’ ‘quantreg’ ‘rlang’ ‘shinyjs’ ‘tidyr’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
Namespaces in Imports field not imported from:
  ‘DBI’ ‘GGally’ ‘RColorBrewer’ ‘Rcpp’ ‘assertthat’ ‘backports’
  ‘colorspace’ ‘colourpicker’ ‘evaluate’ ‘futile.options’ ‘gdtools’
  ‘gtable’ ‘htmltools’ ‘htmlwidgets’ ‘httpuv’ ‘labeling’ ‘lambda.r’
  ‘lazyeval’ ‘magrittr’ ‘miniUI’ ‘munsell’ ‘plyr’ ‘reshape’ ‘rprojroot’
  ‘scales’ ‘stringi’ ‘stringr’ ‘svglite’ ‘tibble’ ‘xtable’ ‘yaml’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Namespace in Imports field not imported from: ‘mockery’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 51.1Mb
  sub-directories of 1Mb or more:
    libs  50.2Mb
installed size is 47.5Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
Package suggested but not available for checking: ‘cplexAPI’
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/gnmf.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘car’ ‘wordcloud’
  All declared Imports should be used.
Running examples in ‘gpg-Ex.R’ failed
The error most likely occurred in:

> ### Name: gpg_sign
> ### Title: PGP Signatures
> ### Aliases: gpg_sign gpg_verify gpg gpg_sign
> 
> ### ** Examples
> 
> # This requires you have the Debian master key in your keyring
> msg <- tempfile()
> sig <- tempfile()
> download.file("http://http.us.debian.org/debian/dists/jessie/Release", msg)
trying URL 'http://http.us.debian.org/debian/dists/jessie/Release'
Content type 'application/octet-stream' length 148406 bytes (144 KB)
==================================================
downloaded 144 KB

> download.file("http://http.us.debian.org/debian/dists/jessie/Release.gpg", sig)
trying URL 'http://http.us.debian.org/debian/dists/jessie/Release.gpg'
Content type 'application/octet-stream' length 2434 bytes
==================================================
downloaded 2434 bytes

> gpg_verify(sig, msg, error = FALSE)
Error: GnuPG detached verification error: General error
Execution halted
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R  19.3Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Namespaces in Imports field not imported from:
  ‘methods’ ‘raster’ ‘rgeos’ ‘sp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘deldir’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘BiasedUrn’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Namespace in Imports field not imported from: ‘rrcov’
  All declared Imports should be used.
Running ‘run-tests.R’
Running the tests in ‘tests/run-tests.R’ failed.
Complete output:
  > library(testthat)
  > library(gWidgets2)
  Loading required package: digest
  > options(guiToolkit="tcltk")
  > 
  > f <- list.files(system.file("tests", package="gWidgets2"), full=T)
  > f <- Filter(function(x) !grepl("README", x), f)
  > f <- Filter(function(x) !grepl("html", x), f)
  > ## issues
  > f <- Filter(function(x) !grepl("df.R", x), f)
  > f <- Filter(function(x) !grepl("text.R", x), f)
  > f <- Filter(function(x) !grepl("tree.R", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/button.R
  Loading required package: gWidgets2tcltk
  Loading required package: memoise
  Loading required package: tcltk
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/calendar.R
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/checkbox.R
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/combobox.R
  testing /data/gannet/ripley/R/test-clang/gWidgets2/tests/containers.R
  Error: svalue(cards) not equal to 1.
  Modes: logical, numeric
  target is logical, current is numeric
  Execution halted
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘foreach’ ‘methods’
  All declared Imports should be used.
installed size is 136.5Mb
  sub-directories of 1Mb or more:
    java  134.8Mb
Running examples in ‘hamlet-Ex.R’ failed
The error most likely occurred in:

> ### Name: mem.powersimu
> ### Title: Power simulations for the fixed effects of a mixed-effects model
> ###   through structured bootstrapping of the data and re-fitting of the
> ###   model
> ### Aliases: mem.powersimu
> ### Keywords: power design mem
> 
> ### ** Examples
> 
> # Use the VCaP ARN data as an example
> data(vcaplong)
> arn <- vcaplong[vcaplong[,"Group"] == "Vehicle" | vcaplong[,"Group"] == "ARN",]
> 
> # lme4 is required for mixed-effects models
> library(lme4)
Loading required package: Matrix
> # Fit an example fixed effects model
> fit <- lmer(PSA ~ 1 + DrugWeek + ARN:DrugWeek + (1|ID) + (0 + DrugWeek|ID), data = arn)
> 
> # For reproducibility, set a seed
> set.seed(123)
> # Run a brief power analysis with only a few selected N values and a limited number of bootstrapping
> # Balance strata over the ARN and non-ARN (=Vehicle) so that both contain equal count of individuals
> power <- mem.powersimu(fit, N=c(4, 7, 10), boot=20, strata="ARN", plot=TRUE)
Error: 'summary' is not an exported object from 'namespace:lmerTest'
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  SNPHWEX.cpp:50:31: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  SNPHWEX.cpp:51:65: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/HardyWeinberg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./City.h:82:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:93:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:94:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:95:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  City.cpp:96:26: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:87:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:89:8: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:267:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  MurmurHash3.cpp:268:23: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ./Spooky.h:285:36: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashFunction.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ../inst/include/hashmap/sparsepp/spp.h:2342:21: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
  ../inst/include/hashmap/sparsepp/spp.h:2365:22: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/hashmap.Rcheck/00install.out’ for details.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Namespace in Imports field not imported from: ‘hms’
  All declared Imports should be used.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Namespaces in Imports field not imported from:
  ‘memoise’ ‘ratelimitr’
  All declared Imports should be used.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        7.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Rdpack’
  All declared Imports should be used.
print.summary.hotspots: warning in sort(x$data, dec = TRUE): partial
  argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$positive, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
print.summary.hotspots: warning in sort(x$disprop$negative, dec =
  TRUE): partial argument match of 'dec' to 'decreasing'
Lchs: no visible global function definition for ‘plot’
Lchs: no visible global function definition for ‘points’
disprop: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘median’
hotspots: no visible global function definition for ‘qnorm’
hotspots: no visible global function definition for ‘qt’
plot.hotspots: no visible global function definition for ‘par’
summary.hotspots: no visible global function definition for ‘median’
Undefined global functions or variables:
  median par plot points qnorm qt
Consider adding
  importFrom("graphics", "par", "plot", "points")
  importFrom("stats", "median", "qnorm", "qt")
to your NAMESPACE file.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.9Mb
    doc   2.5Mb
Found the following significant warnings:
  language.c:41:5: warning: flexible array initialization is a GNU extension [-Wgnu-flexible-array-initializer]
See ‘/data/gannet/ripley/R/packages/tests-clang/htmltidy.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘igraph’
  All declared Imports should be used.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.6Mb
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot2d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'lo' to 'locut'
hyper.plot2d: warning in magmap(seq(sigscale[1], sigscale[2], len =
  100), lo = sigscale[1], hi = sigscale[2], flip = TRUE, type = "num"):
  partial argument match of 'hi' to 'hicut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'lo' to 'locut'
hyper.plot3d: warning in magmap(sigmas, lo = sigscale[1], hi =
  sigscale[2], flip = TRUE, type = "num"): partial argument match of
  'hi' to 'hicut'
Namespace in Imports field not imported from: ‘lattice’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘ggplot2’ ‘pander’
  All declared Imports should be used.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.2Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/IBDsim.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.4Mb
    doc    5.1Mb
    libs  13.0Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  35.4Mb
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.1Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.0Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     30.7Mb
Namespace in Imports field not imported from: ‘jpeg’
  All declared Imports should be used.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R  10.8Mb
Namespace in Imports field not imported from: ‘mediation’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘count_compare’
Namespaces in Imports field not imported from:
  ‘lme4’ ‘reshape2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘rgeos’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Namespace in Imports field not imported from: ‘prodlim’
  All declared Imports should be used.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Namespace in Imports field not imported from: ‘png’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.4Mb
Namespace in Imports field not imported from: ‘irr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘colorRamps’ ‘virtualspecies’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘animation’ ‘comtradr’ ‘ndtv’ ‘statnet’ ‘xergm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘curl’ ‘lubridate’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘fAssets’ ‘timeDate’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘GGally’ ‘GPArotation’ ‘MASS’ ‘PMCMR’ ‘R6’ ‘ROCR’
  ‘afex’ ‘car’ ‘emmeans’ ‘ggridges’ ‘lavaan’ ‘multcomp’ ‘mvnormtest’
  ‘nnet’ ‘psych’ ‘vcd’ ‘vcdExtra’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘nlme’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.7Mb
Namespace in Imports field not imported from: ‘doParallel’
  All declared Imports should be used.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.5Mb
Namespace in Imports field not imported from: ‘mclust’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stinepack’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘EQL’ ‘knitr’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   8.2Mb
Namespaces in Imports field not imported from:
  ‘lme4’ ‘metafor’ ‘nlme’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Package in Depends field not imported from: ‘cluster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R   7.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘tibble’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.7Mb
Namespace in Imports field not imported from: ‘RUnit’
  All declared Imports should be used.
kztp: warning in rowMeans(kztp, dim = 2): partial argument match of
  'dim' to 'dims'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/LambertW.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘repr’
  All declared Imports should be used.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs          13.9Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    geojson  11.9Mb
Namespace in Imports field not imported from: ‘rgeos’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘scales’ ‘tibble’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘memoise’
  All declared Imports should be used.
Running examples in ‘lime-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_superpixels
> ### Title: Test super pixel segmentation
> ### Aliases: plot_superpixels
> 
> ### ** Examples
> 
> image <- system.file('extdata', 'produce.png', package = 'lime')
> 
> # plot with default settings
> plot_superpixels(image)

 *** caught segfault ***
address 0x108, cause 'memory not mapped'

Traceback:
 1: magick_image_write_frame(image, format = format, i = i)
 2: image_write_frame(image, format = channels)
 3: image_data(x[i])
 4: `[[.magick-image`(image_channel(im_lab, "R"), 1)
 5: image_channel(im_lab, "R")[[1]]
 6: slic(image_channel(im_lab, "R")[[1]][1, , ], image_channel(im_lab,     "G")[[1]][1, , ], image_channel(im_lab, "B")[[1]][1, , ],     n_sp = n_superpixels, weight = weight, n_iter = n_iter)
 7: plot_superpixels(image)
An irrecoverable exception occurred. R is aborting now ...
Namespace in Imports field not imported from: ‘RColorBrewer’
  All declared Imports should be used.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.1Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.9Mb
    testdata   1.6Mb
lmec: warning in qr.Q(qrZ, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: warning in qr.Q(qra, compl = TRUE): partial argument match of
  'compl' to 'complete'
lmec: no visible global function definition for ‘lm’
lmec: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘dnorm’
lmec : vtrnorm2: no visible global function definition for ‘runif’
lmec : vtrnorm2: no visible global function definition for ‘qnorm’
lmec : vtrnorm2: no visible global function definition for ‘pnorm’
lmec: no visible global function definition for ‘rnorm’
lmec: no visible global function definition for ‘ar’
Undefined global functions or variables:
  ar dnorm lm pnorm qnorm rnorm runif
Consider adding
  importFrom("stats", "ar", "dnorm", "lm", "pnorm", "qnorm", "rnorm",
             "runif")
to your NAMESPACE file.
Running examples in ‘lmem.gwaser-Ex.R’ failed
The error most likely occurred in:

> ### Name: mq.g.diagnostics
> ### Title: Performs molecular markers quality diagnostics.
> ### Aliases: mq.g.diagnostics
> 
> ### ** Examples
> 
> data (QA_geno)
> data (QA_map)
> data (QA_pheno)
> 
> P.data <- QA_pheno
> G.data <- QA_geno
> map.data <- QA_map
> 
> cross.data  <- gwas.cross (P.data, G.data, map.data,
+ cross='gwas', heterozygotes=FALSE)
 --Read the following data:
	 179  individuals
	 811  markers
	 3  phenotypes
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
 --Cross type: bc 
> summary (cross.data)
Warning in summary.cross(cross.data) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
    Doubled haploids

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

    No. chromosomes:    7 
        Autosomes:      1 2 3 4 5 6 7 

    Total markers:      811 
    No. markers:        117 147 153 48 113 101 132 
    Percent genotyped:  99.9 
    Genotypes (%):      AA:41.7  BB:58.3 
> 
> #Marker Quality
> 
> mq.g.diagnostics (crossobj=cross.data,I.threshold=0.1,
+              p.val=0.01,na.cutoff=0.1)
Error in plot.missing(crossobj) : could not find function "plot.missing"
Calls: mq.g.diagnostics -> mq_missinggenotype_plot
Execution halted
Namespace in Imports field not imported from: ‘boot’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘mnormt’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  lsdall.c:2078:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2200:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2209:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2219:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2225:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/logspline.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘NLRoot’ ‘ade4’ ‘glmnet’ ‘lars’ ‘lattice’ ‘logmult’ ‘pdist’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Note: found 143 marked Latin-1 strings
  Note: found 833 marked UTF-8 strings
installed size is 47.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  46.1Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘tcltk2’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘ncdf4’ ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘e1071’ ‘utils’
  All declared Imports should be used.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    TS_files     5.9Mb
    base_files   6.3Mb
installed size is 24.6Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘cmprsk’ ‘colorspace’ ‘etm’ ‘fracdiff’ ‘gtable’ ‘munsell’
  ‘numDeriv’ ‘plyr’ ‘quadprog’ ‘scales’ ‘timeDate’ ‘tseries’ ‘zoo’
  All declared Imports should be used.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs   5.0Mb
Running examples in ‘magick-Ex.R’ failed
The error most likely occurred in:

> ### Name: device
> ### Title: Magick Graphics Device
> ### Aliases: device image_graph image_device image_draw image_capture
> 
> ### ** Examples
> 
> # Regular image
> frink <- image_read("https://jeroen.github.io/images/frink.png")
> 
> # Produce image using graphics device
> fig <- image_graph(res = 96)
> ggplot2::qplot(mpg, wt, data = mtcars, colour = cyl)
> dev.off()
pdf 
  2 
> 
> # Combine
> out <- image_composite(fig, frink, offset = "+70+30")
> print(out)
  format width height colorspace matte filesize density
1    PNG   800    600       sRGB  TRUE        0 +72x+72
> 
> # Or paint over an existing image
> img <- image_draw(frink)
> rect(20, 20, 200, 100, border = "red", lty = "dashed", lwd = 5)
Error in rect(20, 20, 200, 100, border = "red", lty = "dashed", lwd = 5) : 
  Magick: non-conforming drawing primitive definition `rectangle' @ error/draw.c/DrawImage/4126
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 433-442 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Magick: non-conforming drawing primitive definition `rectangle' @ error/draw.c/DrawImage/4126
Execution halted
Namespace in Imports field not imported from: ‘grid’
  All declared Imports should be used.
Installation failed.
See ‘/data/gannet/ripley/R/packages/tests-clang/ManifoldOptim.Rcheck/00install.out’ for details.
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    mapdata  33.4Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.7Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
File ‘maxent/libs/maxent.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 35.9Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Namespaces in Imports field not imported from:
  ‘parallelMap’ ‘reshape2’
  All declared Imports should be used.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespace in Imports field not imported from: ‘glmnet’
  All declared Imports should be used.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   8.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘ggplot2’ ‘lavaan’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘RGtk2’ ‘RNifti’ ‘cairoDevice’ ‘gtools’ ‘jsonlite’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘RColorBrewer’ ‘RODBC’ ‘dplyr’ ‘formattable’ ‘ggplot2’
  ‘ggthemes’ ‘magrittr’ ‘mem’ ‘openxlsx’ ‘plotly’ ‘readxl’ ‘shinyBS’
  ‘shinydashboard’ ‘shinyjs’ ‘shinythemes’ ‘stringi’ ‘stringr’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Namespaces in Imports field not imported from:
  ‘colourpicker’ ‘shinyBS’ ‘shinycssloaders’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Namespace in Imports field not imported from: ‘rattle’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggrepel’ ‘reshape’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘shiny’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.1Mb
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/mets.Rcheck/00install.out’ for details.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  16.2Mb
    misc   1.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
File ‘mFilter/R/zzz.R’:
  .onLoad calls:
    writeLines(strwrap(txt, indent = 4, exdent = 4))

Package startup functions should use ‘packageStartupMessage’ to
  generate messages.
See section ‘Good practice’ in '?.onAttach'.

.onLoad: warning in packageDescription("mFilter", lib = mylib): partial
  argument match of 'lib' to 'lib.loc'
bkfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bkfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
bwfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
cffilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
cffilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.cycle, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x.trend, star = tsp.x[1], frequency =
  tsp.x[3]): partial argument match of 'star' to 'start'
hpfilter: warning in ts(x, star = tsp.x[1], frequency = tsp.x[3]):
  partial argument match of 'star' to 'start'
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  19.7Mb
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘copula’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Namespace in Imports field not imported from: ‘MASS’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DiceDesign’ ‘MaxPro’ ‘doSNOW’ ‘jpeg’
  All declared Imports should be used.
cdf.pval: no visible global function definition for ‘median’
cdf.pval: no visible binding for global variable ‘ecdf’
find_hits: no visible global function definition for ‘na.omit’
mad.scores: no visible global function definition for ‘as.formula’
mad.scores: no visible binding for global variable ‘median’
mad.scores: no visible binding for global variable ‘mad’
rm.outliers: no visible global function definition for ‘as.formula’
rm.outliers: no visible binding for global variable ‘median’
rm.outliers: no visible binding for global variable ‘mad’
Undefined global functions or variables:
  as.formula ecdf mad median na.omit
Consider adding
  importFrom("stats", "as.formula", "ecdf", "mad", "median", "na.omit")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘cluster’ ‘dendextend’ ‘npmv’ ‘utils’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.4Mb
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/missDeaths.Rcheck/00install.out’ for details.
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    data   4.0Mb
Namespace in Imports field not imported from: ‘rjags’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘deSolve’ ‘progress’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘R6’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘foreach’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘iterators’ ‘parallel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sparsepp’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘plotrix’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sads’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.8Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
Namespace in Imports field not imported from: ‘ratelimitr’
  All declared Imports should be used.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘caret’ ‘ggformula’ ‘knitr’ ‘testthat’ ‘tidyverse’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘zoo’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.7Mb
export.summary.mpm: warning in complex(real = x$Rows[, FdimsR[1]], imag
  = x$Rows[, FdimsR[2]]): partial argument match of 'imag' to
  'imaginary'
export.summary.mpm: warning in complex(real = x$Columns[, FdimsC[1]],
  imag = x$Columns[, FdimsC[2]]): partial argument match of 'imag' to
  'imaginary'
.onAttach: no visible global function definition for
  ‘packageDescription’
export.summary.mpm: no visible global function definition for
  ‘write.table’
mpm: no visible binding for global variable ‘median’
plot.mpm: no visible global function definition for ‘rainbow’
plot.mpm: no visible global function definition for ‘quantile’
plot.mpm: no visible global function definition for ‘par’
plot.mpm: no visible global function definition for ‘points’
plot.mpm: no visible global function definition for ‘smoothScatter’
plot.mpm: no visible global function definition for ‘colorRampPalette’
plot.mpm: no visible global function definition for ‘symbols’
plot.mpm: no visible global function definition for ‘text’
plot.mpm: no visible global function definition for ‘lines’
plot.mpm: no visible global function definition for ‘box’
Undefined global functions or variables:
  box colorRampPalette lines median packageDescription par points
  quantile rainbow smoothScatter symbols text write.table
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
  importFrom("graphics", "box", "lines", "par", "points",
             "smoothScatter", "symbols", "text")
  importFrom("stats", "median", "quantile")
  importFrom("utils", "packageDescription", "write.table")
to your NAMESPACE file.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘moments’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 75.8Mb
  sub-directories of 1Mb or more:
    libs  75.6Mb
Namespaces in Imports field not imported from:
  ‘boot’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   3.8Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘knitr’
  All declared Imports should be used.
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    java  13.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
Namespace in Imports field not imported from: ‘biomartr’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    extdata  16.2Mb
Namespace in Imports field not imported from: ‘purrrlyr’
  All declared Imports should be used.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘fields’ ‘mvtnorm’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘mgcv’ ‘stats’
  All declared Imports should be used.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Namespaces in Imports field not imported from:
  ‘htmlTable’ ‘lme4’ ‘stringi’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
Namespaces in Imports field not imported from:
  ‘ProjectTemplate’ ‘devtools’ ‘plyr’ ‘survival’
  All declared Imports should be used.
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.1Mb
    R              5.8Mb
    classic-bugs   1.6Mb
    include        5.8Mb
    tests          1.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘dparser’ ‘inline’ ‘mvtnorm’ ‘vpc’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Namespace in Imports field not imported from: ‘deSolve’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘geosphere’ ‘lwgeom’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘XML’ ‘choroplethr’ ‘choroplethrMaps’ ‘data.table’
  ‘forcats’ ‘hurricaneexposure’ ‘plyr’
  All declared Imports should be used.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Namespace in Imports field not imported from: ‘rJava’
  All declared Imports should be used.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/npcp.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Namespace in Imports field not imported from: ‘rts’
  All declared Imports should be used.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  14.2Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Note: found 13172 marked Latin-1 strings
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    extdata  38.9Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   8.7Mb
File ‘nws/R/zzz.R’:
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

blendOptions: warning in assign(names[i], new[[i]], env = options):
  partial argument match of 'env' to 'envir'
docall: warning in get(as.character(fun), env = .GlobalEnv, mode =
  "function"): partial argument match of 'env' to 'envir'
logMsg: no visible global function definition for ‘flush.console’
nwsPkgInfo: no visible global function definition for
  ‘packageDescription’
initialize,nwsServer: no visible global function definition for
  ‘make.socket’
initialize,nwsServer: no visible global function definition for
  ‘close.socket’
Undefined global functions or variables:
  close.socket flush.console make.socket packageDescription
Consider adding
  importFrom("utils", "close.socket", "flush.console", "make.socket",
             "packageDescription")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘nws/R/workerLoop.R’:
  assign("SleighName", displayName, globalenv())
  assign("SleighNws", nws, globalenv())
  assign("SleighUserNws", userNws, globalenv())
  assign("SleighRank", rank, globalenv())
  assign("SleighWorkerCount", workerCount, globalenv())
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Namespace in Imports field not imported from: ‘readr’
  All declared Imports should be used.
installed size is 97.8Mb
  sub-directories of 1Mb or more:
    libs  97.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Namespaces in Imports field not imported from:
  ‘randomForest’ ‘ranger’
  All declared Imports should be used.
installed size is 147.8Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    137.9Mb
    models    4.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    java     1.2Mb
    models   6.0Mb
Namespace in Imports field not imported from: ‘sf’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Running ‘testthat.R’ [21s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > test_check("openxlsx")
  Loading required package: openxlsx
  ── 1. Error: loadWorkbook from different sources (@test-read_sources.R#49)  ────
  subscript out of bounds
  1: expect_true(all.equal.Workbook(wb_url, wb_file), "Loading from URL vs local not equal") at testthat/test-read_sources.R:49
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: all.equal.Workbook(wb_url, wb_file)
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      3.2Mb
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nr' to 'nrow'
bgmm : SplineGMM : moment.conditions: warning in matrix(nr = n.para, nc
  = J): partial argument match of 'nc' to 'ncol'
bgmm: no visible global function definition for ‘ecdf’
bgmm : SplineGMM: no visible global function definition for
  ‘constrOptim’
blr: no visible global function definition for ‘ecdf’
blr: no visible global function definition for ‘constrOptim’
blr: no visible global function definition for ‘lm’
parentcdf : combinations: no visible global function definition for
  ‘combn’
parentcdf : solver: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  combn constrOptim ecdf lm uniroot
Consider adding
  importFrom("stats", "constrOptim", "ecdf", "lm", "uniroot")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
est.lme : <anonymous>: warning in rank(iru, ties = "min"): partial
  argument match of 'ties' to 'ties.method'
est.lme : <anonymous>: no visible global function definition for ‘lme’
est.lme : <anonymous>: no visible global function definition for
  ‘VarCorr’
guo: no visible global function definition for ‘p.adjust’
guo: no visible global function definition for ‘na.omit’
pttest : ptest: no visible global function definition for ‘na.omit’
srt : <anonymous>: no visible global function definition for
  ‘rowttests’
Undefined global functions or variables:
  VarCorr lme na.omit p.adjust rowttests
Consider adding
  importFrom("stats", "na.omit", "p.adjust")
to your NAMESPACE file.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/osc.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running examples in ‘osmplotr-Ex.R’ failed
The error most likely occurred in:

> ### Name: osm_structures
> ### Title: osm_structures
> ### Aliases: osm_structures
> 
> ### ** Examples
> 
> # Default structures:
> osm_structures ()
    structure      key value suffix      cols
1    building building           BU #646464FF
2     amenity  amenity            A #787878FF
3    waterway waterway            W #646478FF
4       grass  landuse grass      G #64A064FF
5     natural  natural            N #647864FF
6        park  leisure  park      P #647864FF
7     highway  highway            H #000000FF
8    boundary boundary           BO #C8C8C8FF
9        tree  natural  tree      T #64A064FF
10 background                          gray20
> # user-defined structures:
> structures <- c ('highway', 'park', 'grass')
> structs <- osm_structures (structures = structures, col_scheme = 'light')
> # make_osm_map returns potentially modified list of data
> dat <- make_osm_map (osm_data = london, structures = structs)
Downloading and extracting OSM data for 1 structures ...

  |                                                                            
  |                                                                      |   0%add_feature() is deprecated; please use add_osm_feature()
Error in check_for_error(doc) : General overpass server error; returned:
OSM3S ResponseThe data included in this document is from www.openstreetmap.org. The data is made available under ODbL.Error: line 8: parse error: ';' expected - ')' found. Error: line 11: parse error: Unexpected end of input. Error: line 8: static error: Element "print" cannot be subelement of element "union". 
Calls: make_osm_map ... extract_osm_objects -> <Anonymous> -> overpass_query -> check_for_error
Execution halted
Package suggested but not available for checking: ‘Rcplex’
Namespace in Imports field not imported from: ‘quantreg’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   2.1Mb
[,ClassW: warning in switch(EXP = i, u1 = {: partial argument match of
  'EXP' to 'EXPR'
[,ClassW: warning in return(x@u1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@u2): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in return(x@w1): partial argument match of 'EXP' to
  'EXPR'
[,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
[<-,ClassW: warning in switch(EXP = i, u1 = {: partial argument match
  of 'EXP' to 'EXPR'
[<-,ClassW: warning in x@u1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, u2 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@u2 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }, w1 = {: partial argument match of 'EXP' to
  'EXPR'
[<-,ClassW: warning in x@w1 <- value: partial argument match of 'EXP'
  to 'EXPR'
[<-,ClassW: warning in }): partial argument match of 'EXP' to 'EXPR'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   5.7Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   9.5Mb
Namespace in Imports field not imported from: ‘ade4’
  All declared Imports should be used.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    lib   9.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘pander’
  All declared Imports should be used.
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    R      2.6Mb
    data   2.1Mb
    libs   6.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Namespace in Imports field not imported from: ‘fda’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Namespaces in Imports field not imported from:
  ‘car’ ‘sandwich’
  All declared Imports should be used.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/Peaks.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘cluster’ ‘graph’
  All declared Imports should be used.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/PhaseType.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘DT’ ‘leaflet’ ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Found the following significant warnings:
  phreeqcpp/cvode.cpp:3783:8: warning: explicitly assigning value of variable of type 'realtype' (aka 'double') to itself [-Wself-assign]
  phreeqcpp/model.cpp:3047:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/model.cpp:3048:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:142:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:155:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:167:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:179:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:193:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/spread.cpp:205:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  phreeqcpp/transport.cpp:630:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/phreeqc.Rcheck/00install.out’ for details.
installed size is 42.0Mb
  sub-directories of 1Mb or more:
    libs  41.3Mb
Namespaces in Imports field not imported from:
  ‘gplots’ ‘phytools’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Namespace in Imports field not imported from: ‘intergraph’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gridExtra’
  All declared Imports should be used.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Namespaces in Imports field not imported from:
  ‘colorspace’ ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘covr’ ‘knitr’
  All declared Imports should be used.
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘Matrix’ ‘RColorBrewer’ ‘arm’ ‘epiDisplay’ ‘foreign’ ‘gbm’
  ‘grid’ ‘lattice’ ‘latticeExtra’ ‘lme4’ ‘nnet’ ‘parallel’ ‘splines’
  ‘survey’ ‘twang’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘hexbin’ ‘quantreg’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘stats’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.0Mb
Namespaces in Imports field not imported from:
  ‘GGally’ ‘PKNCA’ ‘grid’ ‘magrittr’ ‘plyr’ ‘xpose’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Found the following significant warnings:
  heftall.c:1389:2: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lsdall.c:2077:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:505:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:999:21: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  lspecall.c:1078:18: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2199:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2208:12: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2218:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  nlsd.c:2224:9: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/polspline.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      6.4Mb
    data   2.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/data/gannet/ripley/R/packages/tests-clang/powell.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/ppcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/praznik.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Namespace in Imports field not imported from: ‘e1071’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Namespaces in Imports field not imported from:
  ‘DiagrammeRsvg’ ‘RColorBrewer’ ‘tidyr’
  All declared Imports should be used.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.6Mb
Package suggested but not available for checking: ‘qtbase’
Namespaces in Imports field not imported from:
  ‘distcrete’ ‘incidence’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Files which contain pragma(s) suppressing diagnostics:
  ‘src/geobuf.pb.h’ ‘src/rexp.pb.h’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
Namespace in Imports field not imported from: ‘raster’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘forecast’ ‘knitr’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘methods’ ‘pbkrtest’
  All declared Imports should be used.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   2.4Mb
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ptinpoly.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    dict   5.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.3Mb
Namespaces in Imports field not imported from:
  ‘bookdown’ ‘descr’ ‘gee’ ‘lme4’ ‘nlme’ ‘nnet’ ‘ordinal’ ‘pander’
  ‘papeR’ ‘rmdformats’ ‘visreg’
  All declared Imports should be used.
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.2Mb
Compilation used the following non-portable flag(s):
  ‘-Werror=format-security’ ‘-Wp,-D_FORTIFY_SOURCE=2’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.7Mb
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/QPot.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.8Mb
    doc       2.9Mb
    libs      1.4Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs  12.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   4.9Mb
Namespace in Imports field not imported from: ‘psych’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MCMCpack’ ‘gridExtra’ ‘knitr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘data.table’ ‘dplyr’ ‘lmerTest’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   3.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘dtplyr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: ggplot2
Loading required package: plotrix
Warning: Computation failed in `stat_boxplot()`:
there is no package called 'quantreg'
Warning: Computation failed in `stat_boxplot()`:
there is no package called 'quantreg'
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 246.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.1Mb
Running examples in ‘RAtmosphere-Ex.R’ failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: suncalc
> ### Title: Sunrise and Sunset calculations
> ### Aliases: suncalc
> ### Keywords: sun sunset sunrise
> 
> ### ** Examples
> 
> t<-Sys.time()+seq(-3600*12,3600*12,,by=600)
> t0=as.POSIXlt(Sys.time(),tz='UTC')
> plot(t,90-SZA(t,Lat=0,Lon=0),main='SZA',xlab='Time',ylab='El [°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
Namespace in Imports field not imported from: ‘lme4’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO
Warning in postForm(url, .params = params, .opts = opts, binary = binary) :
  No inputs passed to form

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 8 
Error in queryJSON("/web/analysis", params = c(jobID = jobID, de = analysisName,  : 
  Internal server error: java.lang.NullPointerException
Execution halted
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    blp    7.1Mb
    libs   7.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/data/gannet/ripley/R/packages/tests-clang/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ROpenOffice’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   3.0Mb
    po    2.2Mb
Running examples in ‘rcongresso-Ex.R’ failed
The error most likely occurred in:

> ### Name: fetch_despesas_deputado
> ### Title: Fetches expenditures from deputy using its id
> ### Aliases: fetch_despesas_deputado
> 
> ### ** Examples
> 
> gastos_abel_mesquita <- fetch_despesas_deputado(dep_id = 178957)
Error in .congresso_api(.$path, query) : Bad Request (HTTP 400).
Calls: fetch_despesas_deputado ... overscope_eval_next -> .congresso_api -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 45-50 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
Not Found (HTTP 404).
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
    libs      1.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/data/gannet/ripley/R/packages/tests-clang/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    include  25.5Mb
    libs      1.8Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    include   7.9Mb
    libs     23.5Mb
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    include   1.9Mb
    lib      39.2Mb
    libs     11.3Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   7.0Mb
    libs      2.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs     14.0Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.4Mb
    libs      4.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  cwb/cqp/corpmanag.c:1832:12: warning: comparison of function 'split_subcorpus_name' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/rcqp.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘smcure’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rcompression’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/rdist.Rcheck/00install.out’ for details.
Subdirectory ‘src’ contains:
  CLRApi.hpp CLRFactory.hpp CLRObjectRef.hpp Common.hpp OS.hpp
  RValue.hpp TcpClient.hpp
These are unlikely file names for src files.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Namespace in Imports field not imported from: ‘digest’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 16-19 (rDVR-basics.Rmd) 
Error: processing vignette 'rDVR-basics.Rmd' failed with diagnostics:
there is no package called 'RSelenium'
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.6Mb
Found the following apparent object files/libraries:
  inst/obj/cube.obj inst/obj/cube_badmtl.obj
Object files/libraries should not be included in a source package.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Note: found 1 marked Latin-1 string
  Note: found 1 marked UTF-8 string
  Note: found 7 strings marked as "bytes"
xy: warning in assign(xname, X, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
xy: warning in assign(yname, y, env = .GlobalEnv): partial argument
  match of 'env' to 'envir'
bestmods: no visible global function definition for ‘abline’
bestmods: no visible global function definition for ‘axis’
bestmods: no visible global function definition for ‘lines’
cic: no visible global function definition for ‘lsfit’
cic: no visible global function definition for ‘var’
cvic: no visible global function definition for ‘lsfit’
cvic: no visible global function definition for ‘lm’
eic: no visible global function definition for ‘lsfit’
eic: no visible global function definition for ‘lm’
ic.min: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘lsfit’
scoremods: no visible global function definition for ‘var’
xy: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline axis lines lm lsfit rnorm var
Consider adding
  importFrom("graphics", "abline", "axis", "lines")
  importFrom("stats", "lm", "lsfit", "rnorm", "var")
to your NAMESPACE file.

Found the following assignments to the global environment:
File ‘reams/R/xy.R’:
  assign(xname, X, env = .GlobalEnv)
  assign(yname, y, env = .GlobalEnv)
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.8Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.8Mb
Namespace in Imports field not imported from: ‘DBI’
  All declared Imports should be used.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.5Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.8Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘nnet’ ‘purrr’
  All declared Imports should be used.
Package which this enhances but not available for checking: ‘Rcplex’
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Namespaces in Imports field not imported from:
  ‘compiler’ ‘data.table’
  All declared Imports should be used.
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/repeated.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘methods’
  All declared Imports should be used.
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    libs  50.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.3Mb
Namespace in Imports field not imported from: ‘RcppProgress’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
Rjava.init.warning: stack size reduced from unlimited to 7957504 bytes after JVM initialization.
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.5Mb
    libs   8.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc   9.8Mb
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RHRV.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘gWidgetsRGtk2’
  All declared Imports should be used.
Found the following significant warnings:
  computePvals.c:488:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/ridge.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘rlang’
  All declared Imports should be used.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Namespace in Imports field not imported from: ‘crul’
  All declared Imports should be used.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONGlobals.h:44:49: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONValidator.cpp:394:105: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  JSONValidator.cpp:397:104: warning: empty macro arguments are a C99 feature [-Wc99-extensions]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/data/gannet/ripley/R/packages/tests-clang/RJSONIO.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    datasets  10.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    rmd   6.1Mb
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘_ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’
File ‘RMC/libs/RMC.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmweather)
  > 
  > test_check("rmweather")
  ── 1. Failure: Test training function (@test_02_rmw_functions.R#53)  ───────────
  model$r.squared not equal to 0.4184627.
  1/1 mismatches
  [1] 0.399 - 0.418 == -0.0196
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: Test training function (@test_02_rmw_functions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Found the following significant warnings:
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:172:13: warning: variable length arrays are a C99 feature [-Wvla-extension]
  /data/gannet/ripley/R/test-clang/progress/include/RProgress.h:220:16: warning: variable length arrays are a C99 feature [-Wvla-extension]
See ‘/data/gannet/ripley/R/packages/tests-clang/rncl.Rcheck/00install.out’ for details.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
installed size is 97.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    R   9.7Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/robfilter.Rcheck/00install.out’ for details.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
o.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
p.rocc: warning in factor(pr, level = c(0, 1)): partial argument match
  of 'level' to 'levels'
o.rocc: no visible global function definition for ‘prediction’
o.rocc: no visible global function definition for ‘performance’
o.rocc: no visible global function definition for ‘binom.test’
tr.rocc: no visible global function definition for ‘prediction’
tr.rocc: no visible global function definition for ‘performance’
Undefined global functions or variables:
  binom.test performance prediction
Consider adding
  importFrom("stats", "binom.test")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
Namespace in Imports field not imported from: ‘matrixcalc’
  All declared Imports should be used.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘httpuv’ ‘utils’
  All declared Imports should be used.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.5Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   4.2Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.3Mb
Namespace in Imports field not imported from: ‘htmltools’
  All declared Imports should be used.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.3Mb
Namespace in Imports field not imported from: ‘vegan’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: robustbase
Scalable Robust Estimators with High Breakdown Point (version 1.4-3)

Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Warning in arrows(0, 0, y[, 1L] * 0.8, y[, 2L] * 0.8, col = col[[2L]], length = arrow.len) :
  zero-length arrow is of indeterminate angle and so skipped
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rrcov.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘biwavelet’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-clang/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/data/gannet/ripley/R/packages/tests-clang/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Namespace in Imports field not imported from: ‘gdalUtils’
  All declared Imports should be used.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 52.5Mb
  sub-directories of 1Mb or more:
    libs  51.9Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Namespace in Imports field not imported from: ‘pkgconfig’
  All declared Imports should be used.
installed size is 157.3Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    doc     2.9Mb
    libs  152.5Mb
installed size is 293.7Mb
  sub-directories of 1Mb or more:
    libs  291.1Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Namespace in Imports field not imported from: ‘mc2d’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    Lib  11.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
Namespaces in Imports field not imported from:
  ‘RSQLite’ ‘stats’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘rmarkdown’
  All declared Imports should be used.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.0Mb
Namespace in Imports field not imported from: ‘RGtk2’
  All declared Imports should be used.
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
rvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Package suggested but not available for checking: ‘gpuR’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
    test  19.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.6Mb
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxCEcolInf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./lsoda_internal.h:21:113: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  lsoda.c:107:13: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
  lsoda.c:119:13: warning: token pasting of ',' and __VA_ARGS__ is a GNU extension [-Wgnu-zero-variadic-macro-arguments]
See ‘/data/gannet/ripley/R/packages/tests-clang/RxODE.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   7.2Mb
Namespace in Imports field not imported from: ‘n1qn1’
  All declared Imports should be used.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: result of comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/Ryacas.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs    7.5Mb
    yacas   1.5Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Namespace in Imports field not imported from: ‘spanel’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘subplex’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SafeBayes.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
Namespaces in Imports field not imported from:
  ‘purrr’ ‘tidyr’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Namespace in Imports field not imported from: ‘pvclust’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘cowplot’ ‘ggplot2’ ‘ggridges’ ‘ggstance’ ‘jmvcore’
  All declared Imports should be used.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.7Mb
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘testthat’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘gbm’
  All declared Imports should be used.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SDMTools.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/data/gannet/ripley/R/packages/tests-clang/Segmentor3IsBack.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘cluster’ ‘factoextra’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘FD’
  All declared Imports should be used.
predict.SEL: warning in splineDesign(newdata, knots = knts, ord =
  object$nord, deriv = rep(deriv, length(newdata)), outer.ok = TRUE):
  partial argument match of 'deriv' to 'derivs'
getbinPost: no visible binding for global variable ‘dbeta’
getbinPost: no visible binding for global variable ‘pbeta’
getbinPost : fu: no visible global function definition for ‘dbinom’
getbinPost : fu: no visible global function definition for ‘predict’
getbinPost: no visible global function definition for ‘integrate’
getbinPost: no visible global function definition for ‘splinefun’
int.funct: no visible global function definition for ‘integrate’
int.funct2: no visible global function definition for ‘integrate’
min.abs: no visible global function definition for ‘uniroot’
plot.SEL: no visible global function definition for ‘plot’
print.SEL: no visible global function definition for ‘integrate’
print.summary.SEL : foo1: no visible global function definition for
  ‘predict’
print.summary.SEL : foo2: no visible global function definition for
  ‘predict’
print.summary.SEL: no visible global function definition for
  ‘integrate’
quantSEL: no visible global function definition for ‘predict’
quantSEL: no visible global function definition for ‘splinefun’
rvSEL: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dbeta dbinom integrate pbeta plot predict runif splinefun uniroot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dbeta", "dbinom", "integrate", "pbeta", "predict",
             "runif", "splinefun", "uniroot")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘purrr’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘XML’ ‘mgcv’
  All declared Imports should be used.
Running examples in ‘seoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: lastCached
> ### Title: Function to get the last Google Cache Date for a URL
> ### Aliases: lastCached
> 
> ### ** Examples
> 
> lastCached("https://www.r-project.org/")
Error in if (is.na(res)) { : argument is of length zero
Calls: lastCached
Execution halted
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs  12.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/seqminer.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
capture: no visible binding for global variable ‘resultText’
restore.session: no visible binding for global variable
  ‘.save.session.packages’
restore.session: no visible binding for global variable
  ‘.save.session.search’
save.session: no visible global function definition for ‘dev.list’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.search’
save.session: no visible binding for '<<-' assignment to
  ‘.save.session.packages’
Undefined global functions or variables:
  .save.session.packages .save.session.search dev.list resultText
Consider adding
  importFrom("grDevices", "dev.list")
to your NAMESPACE file.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    libs     6.1Mb
    sqlite   1.5Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   3.3Mb
Namespace in Imports field not imported from: ‘parallel’
  All declared Imports should be used.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
Namespace in Imports field not imported from: ‘shiny’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinydashboard’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘htmlwidgets’ ‘jsonlite’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
  ‘shinyBS’ ‘xtable’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KGode’ ‘XML’ ‘ggplot2’ ‘gridExtra’ ‘mvtnorm’ ‘reshape2’ ‘shinyjs’
  All declared Imports should be used.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    www   6.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘viridis’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘MASS’ ‘class’ ‘cluster’ ‘lattice’ ‘nnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘grid’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  10.9Mb
File ‘simpleboot/R/zzz.R’:
  .onLoad calls:
    require(boot)

Package startup functions should not change the search path.
See section ‘Good practice’ in '?.onAttach'.

lo.boot.resample: warning in sample(1:nrow(orig.data), rep = TRUE, prob
  = weights): partial argument match of 'rep' to 'replace'
lo.boot.resample: warning in sample(res, rep = TRUE, prob = weights):
  partial argument match of 'rep' to 'replace'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.9Mb
Namespaces in Imports field not imported from:
  ‘BB’ ‘MASS’ ‘ggplot2’ ‘grid’ ‘triangle’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘metafor’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘pracma’
  All declared Imports should be used.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.8Mb
Namespace in Imports field not imported from: ‘mcmc’
  All declared Imports should be used.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
installed size is 43.1Mb
  sub-directories of 1Mb or more:
    libs  41.8Mb
Note: found 15 marked Latin-1 strings
  Note: found 2 marked UTF-8 strings
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   8.1Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/SMCP.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘compiler’ ‘lmtest’
  All declared Imports should be used.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.2Mb
Namespaces in Imports field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  All declared Imports should be used.
Found the following significant warnings:
  /usr/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /usr/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/data/gannet/ripley/R/packages/tests-clang/SnakeCharmR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./snappy-stubs-internal.h:95:51: warning: 'long long' is a C++11 extension [-Wc++11-long-long]
See ‘/data/gannet/ripley/R/packages/tests-clang/snappier.Rcheck/00install.out’ for details.
Running examples in ‘SNPtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: categorize.variants
> ### Title: categorize.variants
> ### Aliases: categorize.variants
> 
> ### ** Examples
> 
>   data(example.snps)
>   snp.type = categorize.variants(variants = example.snps[1:50,])
Error in open.TabixFile(con) : 
  [khttp_connect_file] fail to open file (HTTP code: 404).
Calls: categorize.variants -> get.mgi.features -> open -> open.TabixFile
Execution halted
Error in re-building vignettes:
  ...
Loading required package: IRanges
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, mapply, match, mget, order, paste,
    pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans, rowSums,
    rownames, sapply, setdiff, sort, table, tapply, union, unique,
    unsplit, which, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: Rsamtools

Error: processing vignette 'SNPtools.Rnw' failed with diagnostics:
 chunk 3 
Error in open.TabixFile(con) : 
  [khttp_connect_file] fail to open file (HTTP code: 404).

Execution halted
Namespaces in Imports field not imported from:
  ‘gtools’ ‘hashmap’ ‘reshape2’
  All declared Imports should be used.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
Namespaces in Imports field not imported from:
  ‘devtools’ ‘rstudioapi’
  All declared Imports should be used.
Running ‘test-all.R’ [191s/228s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Failure: simList object initializes correctly (@test-simList.R#17)  ──────────────────────────
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘fastdigest’ ‘httr’
  All declared Imports should be used.
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  34.4Mb
Namespace in Imports field not imported from: ‘foreach’
  All declared Imports should be used.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Namespace in Imports field not imported from: ‘lubridate’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘SpatialEpi’ ‘dplyr’ ‘dygraphs’ ‘ggplot2’
  ‘htmlwidgets’ ‘knitr’ ‘leaflet’ ‘mapproj’ ‘maptools’ ‘rgdal’ ‘rgeos’
  ‘rmarkdown’ ‘shinyjs’ ‘spdep’ ‘xts’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘moments’ ‘poweRlaw’
  All declared Imports should be used.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.7Mb
    help   5.0Mb
    libs   1.8Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.2Mb
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nr' to 'nrow'
spe: warning in matrix(retlist[[10]], nr = nobs, nc = edim): partial
  argument match of 'nc' to 'ncol'
spe: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Namespace in Imports field not imported from: ‘maptools’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘class’ ‘mlbench’
  All declared Imports should be used.
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Error in re-building vignettes:
  ...
## ----- This is spikeSlabGAM 1.1-11 ----- ##
Please note that a recent update to gridExtra has made it necessary
  to change the interface for <plot.spikeSlabGAM> starting in version 1.1-9.
Instead of arguments 'rows', 'cols', 'widths', 'heights', 'maxPlotsPerPage',
  it now accepts only 'nrow' and 'ncol'.
Arguments 'widths' & 'heights' can still be defined and are handed over
  to <gridExtra:::marrangeGrob>.
Sorry for the inconvenience.
Loading required package: parallel
Loading required package: stabs
This is mboost 2.8-1. See 'package?mboost' and 'news(package  = "mboost")'
for a complete list of changes.


Attaching package: 'ggplot2'

The following object is masked from 'package:mboost':

    %+%

Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots,  :
  Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used.
Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘splitstackshape-Ex.R’ failed
The error most likely occurred in:

> ### Name: cSplit_f
> ### Title: Split Concatenated Cells in a data.frame or a data.table
> ### Aliases: cSplit_f
> 
> ### ** Examples
> 
> 
> ## Sample data. Change `n` to larger values to test on larger data
> set.seed(1)
> n <- 10
> mydf <- data.frame(id = sequence(n))
> mydf <- within(mydf, {
+   v3 <- do.call(paste, c(data.frame(matrix(sample(
+   letters, n*4, TRUE), ncol = 4)), sep = "_"))
+   v2 <- do.call(paste, c(data.frame(matrix(sample(
+   LETTERS, n*3, TRUE), ncol = 3)), sep = "."))
+   v1 <- do.call(paste, c(data.frame(matrix(sample(
+   10, n*2, TRUE), ncol = 2)), sep = "-"))
+ })
> mydf
   id   v1    v2      v3
1   1  4-5 V.M.X g_f_y_m
2   2  9-8 Q.W.H j_e_f_p
3   3  4-4 U.L.L o_r_q_m
4   4  4-4 O.G.I x_j_d_e
5   5  5-8 N.B.Q f_u_g_v
6   6  9-3 U.C.G x_m_k_r
7   7  9-8 A.I.M y_s_a_u
8   8  4-2 M.N.T r_z_j_c
9   9  8-3 T.R.C q_j_w_s
10 10 10-2 S.K.W b_u_i_k
> 
> cSplit_f(mydf, splitCols = c("v1", "v2", "v3"), sep = c("-", ".", "_"))
Error in fread(x, sep[i], header = FALSE) : 
  You can provide 'input=' or 'file=', not both.
Calls: cSplit_f -> fread
Execution halted
Unknown package ‘antaresViz’ in Rd xrefs
Namespace in Imports field not imported from: ‘biomod2’
  All declared Imports should be used.
Note: found 8 marked Latin-1 strings
  Note: found 83 marked UTF-8 strings
installed size is 13.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.0Mb
Namespaces in Imports field not imported from:
  ‘BayesX’ ‘BayesXsrc’ ‘automap’ ‘plyr’ ‘rgdal’ ‘splines’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘viridisLite’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘shinyFiles’
  All declared Imports should be used.
stkde: no visible global function definition for ‘npudensbw’
stkde: no visible global function definition for ‘npudens’
stkde: no visible global function definition for ‘quantile’
stkde: no visible global function definition for ‘heat.colors’
stkde: no visible global function definition for ‘par’
stkde: no visible global function definition for ‘image’
stkde: no visible global function definition for ‘contour’
stkde.base: no visible global function definition for ‘npudensbw’
stkde.base: no visible global function definition for ‘npudens’
stkde.sig: no visible global function definition for ‘SpatialPoints’
stkde.sig: no visible global function definition for ‘spsample’
stkde.sig: no visible global function definition for ‘bbox’
stkde.sig: no visible global function definition for ‘quantile’
stkde.sig: no visible global function definition for ‘heat.colors’
stkde.sig: no visible global function definition for ‘par’
stkde.sig: no visible global function definition for ‘image’
stkde.sig: no visible global function definition for ‘contour’
Undefined global functions or variables:
  SpatialPoints bbox contour heat.colors image npudens npudensbw par
  quantile spsample
Consider adding
  importFrom("grDevices", "heat.colors")
  importFrom("graphics", "contour", "image", "par")
  importFrom("stats", "quantile")
to your NAMESPACE file.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    include   9.1Mb
    lib       1.5Mb
Namespaces in Imports field not imported from:
  ‘readr’ ‘tools’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Namespace in Imports field not imported from: ‘MCMCpack’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StatCharrms.tex' failed.
LaTeX errors:
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
! FancyVerb Error:
  Extraneous input `	\end{}' between \end{RBox} and line end
.
\FV@Error ... {FancyVerb Error:
\space \space #1
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘magrittr’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘stringr’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Namespaces in Imports field not imported from:
  ‘SnowballC’ ‘tm’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘huge’ ‘scales’ ‘shinyjs’
  All declared Imports should be used.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.0Mb
    datasets   2.6Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Namespace in Imports field not imported from: ‘knitcitations’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘sna’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Namespaces in Imports field not imported from:
  ‘broom’ ‘car’ ‘lmerTest’ ‘pbkrtest’
  All declared Imports should be used.
Running ‘testthat.R’ [8s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  ── 1. Error: child process is terminated in Linux (@test-termination.R#85)  ────
  is_process_handle(handle) is not TRUE
  1: expect_true(wait_until_appears(child_id)) at testthat/test-termination.R:85
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: wait_until_appears(child_id)
  5: process_wait(handle, TIMEOUT_IMMEDIATE) at /data/gannet/ripley/R/packages/tests-clang/subprocess.Rcheck/tests/testthat/helper-processes.R:58
  6: stopifnot(is_process_handle(handle))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 71 SKIPPED: 2 FAILED: 1
  1. Error: child process is terminated in Linux (@test-termination.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘fields’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RColorBrewer’ ‘classInt’ ‘grDevices’ ‘graphics’ ‘pixmap’ ‘rgeos’
  ‘sp’
  All declared Imports should be used.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/data/gannet/ripley/R/packages/tests-clang/SuppDists.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
installed size is 69.6Mb
  sub-directories of 1Mb or more:
    libs  68.7Mb
Namespace in Imports field not imported from: ‘cowplot’
  All declared Imports should be used.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
Namespace in Imports field not imported from: ‘quadprog’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/svd.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable ‘iset’ in DATA statement at (1)
  Warning: GNU Extension: Variable ‘iset’ at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: GNU Extension: Missing comma at (1)
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘cnop’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/data/gannet/ripley/R/packages/tests-clang/SWATmodel.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘lazyeval’ ‘lubridate’ ‘tidyr’
  All declared Imports should be used.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.1Mb
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘PerformanceAnalytics’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    tklibs   4.9Mb
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: sn
Loading required package: stats4

Attaching package: 'sn'

The following object is masked from 'package:stats':

    sd

Loading required package: mclust
Package 'mclust' version 5.4
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: cluster
Warning in .tkmeans.warn(O, ret) :
  Clusters with size < n * 0.02 found - try reducing k.
Warning in .tclust.warn(O, O$ret) :
  The result is artificially constrained due to restr.fact = 12.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tclust.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte sequence.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    sql   8.6Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    apps   2.6Mb
    libs   1.5Mb
Namespaces in Imports field not imported from:
  ‘data.table’ ‘datasets’ ‘stats’
  All declared Imports should be used.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.9Mb
Namespaces in Imports field not imported from:
  ‘nlme’ ‘tidyr’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Namespace in Imports field not imported from: ‘rprojroot’
  All declared Imports should be used.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   5.3Mb
Namespace in Imports field not imported from: ‘irlba’
  All declared Imports should be used.
Note: found 10051 marked UTF-8 strings
  Note: found 10523 strings marked as "bytes"
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    rda    3.8Mb
Namespaces in Imports field not imported from:
  ‘gridExtra’ ‘splancs’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(tidyinftheo)
  > 
  > test_check("tidyinftheo")
  ── 1. Error: right number of columns given (@test-errors.R#10)  ────────────────
  argument "expr" is missing, with no default
  1: expect_length(tab %>% select(vs) %>% shannon_entropy(), 1) at testthat/test-errors.R:10
  2: quasi_label(enquo(object))
  3: eval_bare(get_expr(quo), get_env(quo))
  4: tab %>% select(vs) %>% shannon_entropy()
  5: withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
  6: eval(quote(`_fseq`(`_lhs`)), env, env)
  7: eval(quote(`_fseq`(`_lhs`)), env, env)
  8: `_fseq`(`_lhs`)
  9: freduce(value, `_function_list`)
  10: withVisible(function_list[[k]](value))
  11: function_list[[k]](value)
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘dbplyr’ ‘reprex’ ‘rlang’
  All declared Imports should be used.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/data/gannet/ripley/R/packages/tests-clang/TimeMachine.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘devtools’ ‘forecast’
  All declared Imports should be used.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         3.7Mb
    rmarkdown   1.3Mb
Namespaces in Imports field not imported from:
  ‘rvest’ ‘xml2’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘broom’ ‘tibble’
  All declared Imports should be used.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    examples  14.9Mb
    include    3.0Mb
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Namespaces in Imports field not imported from:
  ‘R6’ ‘jmvcore’
  All declared Imports should be used.
Note: found 42 marked Latin-1 strings
  Note: found 360 marked UTF-8 strings
File ‘tpr/libs/tpr.so’:
  Found ‘_ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’
File ‘tpr/libs/tpr.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
Namespace in Imports field not imported from: ‘neuralnet’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lme4’ ‘nlme’
  All declared Imports should be used.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   4.7Mb
installed size is 37.5Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Namespace in Imports field not imported from: ‘gsDesign’
  All declared Imports should be used.
Namespace in Imports field not imported from: ‘forecast’
  All declared Imports should be used.
covTranspose11: warning in glasso(sc, 2 * rhoc/n, wi.init = gc$wi,
  w.init = gc$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
covTranspose11: warning in glasso(sr, 2 * rhor/p, wi.init = gr$wi,
  w.init = gr$w, maxit = maxit.glasso, thr = thr.glasso, penalize.diag
  = pen.diag): partial argument match of 'penalize.diag' to
  'penalize.diagonal'
.help.ESS: no visible global function definition for ‘index.search’
TransSphere : ttin: no visible global function definition for ‘t.test’
TransSphere: no visible global function definition for ‘sd’
TransSphere: no visible global function definition for ‘quantile’
TransSphere: no visible global function definition for ‘pt’
Undefined global functions or variables:
  index.search pt quantile sd t.test
Consider adding
  importFrom("stats", "pt", "quantile", "sd", "t.test")
to your NAMESPACE file.
installed size is 30.1Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       22.3Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.6Mb
Namespace in Imports field not imported from: ‘mcmcplots’
  All declared Imports should be used.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    data  26.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
Namespaces in Imports field not imported from:
  ‘RCurl’ ‘stringdist’ ‘utils’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Quitting from lines 92-93 (regress_intro.Rmd) 
Error: processing vignette 'regress_intro.Rmd' failed with diagnostics:
object 'ttodth' not found
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Namespaces in Imports field not imported from:
  ‘Rdpack’ ‘maptools’ ‘rgeos’
  All declared Imports should be used.
H: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = H, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
M.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = M.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
Rel.homog: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = Rel.homog, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = list(boots[, , i])):
  partial argument match of 'arg' to 'args'
bootstrap: warning in do.call(what = func, arg = c(abundances =
  list(boots[, , i]), func.arg)): partial argument match of 'arg' to
  'args'
d: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = d, func.arg = list(func.arg), boot.arg)):
  partial argument match of 'arg' to 'args'
sim.groups: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
sim.table: warning in do.call(what = bootstrap, arg = c(abundances =
  list(rbind(scores[i, ], scores[j, ])), func = similarity, func.arg =
  list(func.arg), boot.arg)): partial argument match of 'arg' to 'args'
similarity: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = similarity, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
turnover: warning in do.call(what = bootstrap, arg = c(abundances =
  list(abundances), func = turnover, func.arg = list(func.arg),
  boot.arg)): partial argument match of 'arg' to 'args'
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           4.8Mb
    htmlwidgets   3.7Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    extdata  10.8Mb
Namespaces in Imports field not imported from:
  ‘iterators’ ‘knitr’ ‘purrr’ ‘testthat’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘XML’ ‘checkmate’ ‘gstat’ ‘intervals’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘lubridate’ ‘tibble’
  All declared Imports should be used.
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  50.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Namespaces in Imports field not imported from:
  ‘DT’ ‘ENMeval’ ‘RColorBrewer’ ‘dismo’ ‘dplyr’ ‘leaflet.extras’
  ‘maptools’ ‘raster’ ‘rgdal’ ‘rgeos’ ‘shinyjs’ ‘shinythemes’ ‘spThin’
  ‘spocc’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘R6’ ‘WRS2’ ‘ggplot2’
  All declared Imports should be used.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    client   9.6Mb
    doc      1.0Mb
Namespace in Imports field not imported from: ‘moonBook’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘MASS’ ‘minqa’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'wgsea.tex' failed.
LaTeX errors:
! Package inputenc Error: Invalid UTF-8 byte 252.

See the inputenc package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/data/gannet/ripley/R/packages/tests-clang/WhopGenome.Rcheck/00install.out’ for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Namespaces in Imports field not imported from:
  ‘drc’ ‘imputeTestbench’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘RandomFields’ ‘data.table’
  All declared Imports should be used.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    data  12.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data  14.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    bin   5.4Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Namespaces in Imports field not imported from:
  ‘Amelia’ ‘MatchIt’ ‘WhatIf’
  All declared Imports should be used.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggplot2’ ‘lubridate’
  All declared Imports should be used.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.7Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
asp: no visible global function definition for ‘as.formula’
asp: no visible global function definition for ‘var’
aspm: no visible binding for global variable ‘X.Declan’
aspm: no visible binding for global variable ‘Z.Jaida’
aspm: no visible binding for global variable ‘group.vec.Handan’
aspm: no visible global function definition for ‘as.formula’
aspm: no visible global function definition for ‘glm’
aspm: no visible global function definition for ‘binomial’
aspm: no visible global function definition for ‘poisson’
Undefined global functions or variables:
  X.Declan Z.Jaida as.formula binomial glm group.vec.Handan poisson var
Consider adding
  importFrom("stats", "as.formula", "binomial", "glm", "poisson", "var")
to your NAMESPACE file.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
Found the following significant warnings:
  ADM3.c:37:12: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:37:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  ADM3.c:54:21: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/ADM3.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Found the following significant warnings:
  Warning: namespace ‘RPostgreSQL’ is not available and has been replaced
See ‘/data/gannet/ripley/R/packages/tests-devel/antaresViz.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R             2.2Mb
    help          1.1Mb
    testScripts   1.3Mb
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See ‘/data/gannet/ripley/R/packages/tests-devel/audio.Rcheck/00install.out’ for details.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   3.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 156.7Mb
  sub-directories of 1Mb or more:
    libs  155.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.3Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  18.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is 53.5Mb
  sub-directories of 1Mb or more:
    libs  52.8Mb
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  29.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 98.1Mb
  sub-directories of 1Mb or more:
    libs  98.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 93.3Mb
  sub-directories of 1Mb or more:
    libs  91.9Mb
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.4Mb
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.2Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
bigglm.RODBC: no visible global function definition for ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘odbcQuery’
bigglm.RODBC : chunk: no visible global function definition for
  ‘sqlGetResults’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbSendQuery’
bigglm,ANY-DBIConnection: no visible global function definition for
  ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbClearResult’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘dbSendQuery’
bigglm,ANY-DBIConnection : chunk: no visible global function definition
  for ‘fetch’
Undefined global functions or variables:
  dbClearResult dbSendQuery fetch odbcQuery sqlGetResults
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 52.6Mb
  sub-directories of 1Mb or more:
    libs  51.4Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is 594.6Mb
  sub-directories of 1Mb or more:
    include    3.2Mb
    lib      591.0Mb
installed size is 134.6Mb
  sub-directories of 1Mb or more:
    libs  134.2Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    bin    4.7Mb
    doc    1.1Mb
    libs   4.7Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
installed size is 151.7Mb
  sub-directories of 1Mb or more:
    libs  151.1Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Running examples in ‘CDECRetrieve-Ex.R’ failed
The error most likely occurred in:

> ### Name: cdec_rt
> ### Title: Get a rating table
> ### Aliases: cdec_rt
> 
> ### ** Examples
> 
> cdec_rt("abj") # get the stage to rating curve for ABJ
Error in open.connection(x, "rb") : 
  Timeout was reached: Connection timed out after 10001 milliseconds
Calls: cdec_rt ... %in% -> cdec_rt_list -> <Anonymous> -> read_html.default
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    extdata   5.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   5.9Mb
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   6.4Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    libs  37.0Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/cstab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/ctsem.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   6.1Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    libs  23.0Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
See ‘/data/gannet/ripley/R/packages/tests-devel/DatABEL.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  39.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    libs  43.0Mb
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  25.0Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    include  16.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.7Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   6.0Mb
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  29.1Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.0Mb
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  19.0Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 49.4Mb
  sub-directories of 1Mb or more:
    libs  48.7Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  27.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  optile.c:3122:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3127:26: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3189:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3192:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3340:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3353:28: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3408:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  optile.c:3411:16: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/extracat.Rcheck/00install.out’ for details.
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/data/gannet/ripley/R/packages/tests-devel/FastRWeb.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  47.6Mb
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs  11.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Running examples in ‘fingertipsR-Ex.R’ failed
The error most likely occurred in:

> ### Name: area_types
> ### Title: Area types
> ### Aliases: area_types
> 
> ### ** Examples
> 
> # Returns a data frame with all levels of area and how they map to one another
> area_types()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 10000 milliseconds
Calls: area_types ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 54-58 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
Timeout was reached: Resolving timed out after 10000 milliseconds
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
4 : * * *4 :Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
 *Loading required namespace: funHDDC

 * *Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4

Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!
Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs  12.9Mb
installed size is 59.3Mb
  sub-directories of 1Mb or more:
    libs  58.9Mb
installed size is 80.8Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     77.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  17.6Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Found the following significant warnings:
  convert_util.cpp:299:20: warning: null destination pointer [-Wformat-overflow=]
  convert_util.cpp:307:20: warning: null destination pointer [-Wformat-overflow=]
  Note: break used in wrong context: no loop is visible 
See ‘/data/gannet/ripley/R/packages/tests-devel/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   4.2Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    help   1.2Mb
    libs   5.0Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.8Mb
.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.7Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  51.0Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.2Mb
Found the following significant warnings:
  calculategphmm.cpp:217:13: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/gphmm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Rothmana.cpp:123:15: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/graphicalVAR.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/gRbase.Rcheck/00install.out’ for details.
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.7Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
normalweight: no visible binding for global variable ‘NW_above’
normalweight: no visible binding for global variable ‘NW_below’
obese: no visible global function definition for ‘data’
obese: no visible binding for global variable ‘OB_above’
obese: no visible binding for global variable ‘OB_below’
overweight: no visible global function definition for ‘data’
overweight: no visible binding for global variable ‘OW_above’
overweight: no visible binding for global variable ‘OW_below’
Undefined global functions or variables:
  NW_above NW_below OB_above OB_below OW_above OW_below data
Consider adding
  importFrom("utils", "data")
to your NAMESPACE file.
Running ‘run-tests.R’
Running the tests in ‘tests/run-tests.R’ failed.
Complete output:
  > library(testthat)
  > library(gWidgets2)
  Loading required package: digest
  > options(guiToolkit="tcltk")
  > 
  > f <- list.files(system.file("tests", package="gWidgets2"), full=T)
  > f <- Filter(function(x) !grepl("README", x), f)
  > f <- Filter(function(x) !grepl("html", x), f)
  > ## issues
  > f <- Filter(function(x) !grepl("df.R", x), f)
  > f <- Filter(function(x) !grepl("text.R", x), f)
  > f <- Filter(function(x) !grepl("tree.R", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /data/gannet/ripley/R/test-3.6/gWidgets2/tests/button.R
  Loading required package: gWidgets2tcltk
  Loading required package: memoise
  Loading required package: tcltk
  testing /data/gannet/ripley/R/test-3.6/gWidgets2/tests/calendar.R
  testing /data/gannet/ripley/R/test-3.6/gWidgets2/tests/checkbox.R
  testing /data/gannet/ripley/R/test-3.6/gWidgets2/tests/combobox.R
  testing /data/gannet/ripley/R/test-3.6/gWidgets2/tests/containers.R
  Error: svalue(cards) not equal to 1.
  Modes: logical, numeric
  target is logical, current is numeric
  Execution halted
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is 29.0Mb
  sub-directories of 1Mb or more:
    libs  28.6Mb
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: no visible global function definition for ‘quantile’
print.tsum: no visible global function definition for ‘printCoefmat’
print.tsum: no visible global function definition for ‘symnum’
tlm: no visible global function definition for ‘formula’
tlm: no visible binding for global variable ‘na.fail’
tlm: no visible global function definition for ‘model.matrix’
tlm: no visible global function definition for ‘model.extract’
tlm: no visible binding for global variable ‘response’
tlm: no visible global function definition for ‘lm.fit’
tlm: no visible global function definition for ‘coef’
tlm: no visible global function definition for ‘resid’
tlm: no visible global function definition for ‘Gamma’
tlm: no visible binding for global variable ‘dofse’
tlm: no visible binding for global variable ‘logLik’
tscore: no visible global function definition for ‘model.extract’
tscore: no visible binding for global variable ‘response’
tscore : <anonymous>: no visible global function definition for
  ‘model.matrix’
tscore: no visible global function definition for ‘resid’
tscore: no visible global function definition for ‘pchisq’
tscore: no visible global function definition for ‘printCoefmat’
tsum: no visible global function definition for ‘pnorm’
tsum: no visible global function definition for ‘pt’
tsum: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  Gamma coef dofse formula lm.fit logLik model.extract model.matrix
  na.fail pchisq pnorm printCoefmat pt quantile resid residuals
  response symnum
Consider adding
  importFrom("stats", "Gamma", "coef", "formula", "lm.fit", "logLik",
             "model.extract", "model.matrix", "na.fail", "pchisq",
             "pnorm", "printCoefmat", "pt", "quantile", "resid",
             "residuals", "symnum")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    highlight   1.1Mb
    libs        6.8Mb
PlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   5.3Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   8.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.4Mb
    doc    5.1Mb
    libs  15.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.3Mb
installed size is 41.5Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  37.0Mb
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.7Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.4Mb
Found the following significant warnings:
  regTree.c:317:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  regTree.c:336:38: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/data/gannet/ripley/R/packages/tests-devel/iJRF.Rcheck/00install.out’ for details.
installed size is 43.5Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     36.6Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
Interpol: no visible global function definition for ‘splinefun’
Undefined global functions or variables:
  splinefun
Consider adding
  importFrom("stats", "splinefun")
to your NAMESPACE file.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  27.0Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   8.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   8.3Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   4.9Mb
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.2Mb
    libs      4.7Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.7Mb
comp.npci: no visible global function definition for ‘qnorm’
epband.fun: no visible global function definition for ‘data’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.90’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.95’
epband.fun: no visible binding for global variable
  ‘critical.value.nair.99’
hall.wellner.fun: no visible global function definition for ‘data’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.90’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.95’
hall.wellner.fun: no visible binding for global variable
  ‘critical.value.hall.99’
lrt.confints: no visible global function definition for ‘qchisq’
rothman.fun: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  critical.value.hall.90 critical.value.hall.95 critical.value.hall.99
  critical.value.nair.90 critical.value.nair.95 critical.value.nair.99
  data qchisq qnorm
Consider adding
  importFrom("stats", "qchisq", "qnorm")
  importFrom("utils", "data")
to your NAMESPACE file.